How E-Commerce Operators Can Manage Input Tax Credit under GST Section 9(5) Compliance

The Goods and Services Tax framework in India is built on the principle of subsuming multiple indirect taxes into a unified system, ensuring consistent compliance and reduced complexity for businesses. The Central Goods and Services Tax Act, 2017, is the primary legislation governing the levy and collection of GST on intra-state supplies. While most taxable transactions place the responsibility of payment on the supplier of goods or services, the Act also includes special provisions where liability is shifted to another party.

One such provision is Section 9(5), which specifies that for certain notified categories of services, the liability to pay GST rests with the e-commerce operator facilitating the supply, even though the actual service provider may be a third party. This mechanism is designed to improve compliance in sectors where service providers are small, dispersed, and harder to monitor directly.

Over time, the government has issued notifications specifying which services fall under Section 9(5). The most well-known example was restaurant services supplied through e-commerce platforms, but additional services have since been included. Understanding how Section 9(5) operates is essential for any business engaged in facilitating services through an online platform.

Role of E-Commerce Operators in Indirect Taxation

An e-commerce operator is any person who owns, operates, or manages a digital or electronic facility or platform for electronic commerce. These operators provide a marketplace for service providers and customers to connect, and in many cases, they handle payment processing, logistics coordination, and dispute resolution.

In the GST regime, e-commerce operators are typically responsible for collecting tax at source under Section 52 when facilitating taxable supplies. However, when it comes to Section 9(5), the responsibility becomes more direct: the operator itself must pay the GST as if it were the supplier. This is a significant shift in responsibility and comes with its own compliance obligations.

The rationale for imposing this liability on the operator is that such platforms have better systems for tax collection, reporting, and payment than many of the small-scale providers who use them. As a result, the government ensures more efficient tax compliance and reduces the risk of revenue leakage.

Overview of Services Notified under Section 9(5)

The government has identified specific services for which the Section 9(5) mechanism applies. Initially, this covered certain passenger transportation services provided through platforms, such as radio taxi or motorcab aggregation. Later, restaurant services provided through e-commerce platforms were brought under the provision. Other services have been added over time, depending on compliance challenges and revenue considerations.

When a service is notified under Section 9(5), the actual service provider is deemed not liable to pay GST for that transaction. Instead, the e-commerce operator facilitating the transaction is treated as the supplier for tax purposes and must pay GST on the entire value of the supply.

For instance, if a customer orders food from a restaurant through a digital platform, the platform is treated as the supplier for GST purposes on that order. The restaurant still provides the service in practical terms, but from a taxation perspective, the liability rests entirely on the platform.

How Circular No. 240/34/2024-GST Builds on Previous Clarifications

Circular No. 240/34/2024-GST was issued by the Central Board of Indirect Taxes and Customs to clarify the treatment of input tax credit for e-commerce operators in relation to Section 9(5) services. This clarification was necessary because operators often deal with a combination of their own services and notified services, leading to uncertainty in credit utilization.

Previously, Circular No. 167/23/2021-GST, issued in December 2021, addressed the issue for restaurant services. That circular clarified that while operators could avail input tax credit on inputs and input services used in providing restaurant services, they could not use that credit to discharge their GST liability under Section 9(5) for those services. The liability had to be paid in cash.

The new circular extends this principle beyond restaurant services to all services notified under Section 9(5). This means that while operators can still avail input tax credit for eligible inputs and services, its utilization is restricted for certain liabilities. The rule ensures a clear separation between tax liabilities for notified services and other liabilities, preventing cross-utilization that could undermine the intended cash payment requirement.

Detailed Explanation of Tax Liabilities: Notified Services vs. Own Services

E-commerce operators often have multiple revenue streams. Some of these come from services that fall under Section 9(5), while others are their own taxable supplies unrelated to that provision. Understanding the difference between these two categories is vital for correct GST compliance.

Notified services are those where the operator is legally treated as the supplier. In such cases, the operator must pay GST on the total value of the service provided through the platform, even though the service provider is a third party. This liability must be discharged entirely in cash without using input tax credit.

Own services are those provided by the operator in its own right. Examples include charging commission or facilitation fees to service providers, offering advertising space on the platform, or providing premium features to customers. For these supplies, the operator is the actual supplier, and GST is payable in the ordinary course. Here, the operator can use available input tax credit to offset the liability.

The separation of these liabilities is not merely a theoretical exercise. Operators must maintain accurate records and ensure their GST returns reflect the distinction. Failure to do so can result in penalties and interest for incorrect payment or utilization of credit.

Compliance Obligations for E-Commerce Operators

E-commerce operators covered under Section 9(5) face multiple compliance responsibilities. They must track the value of notified services facilitated through their platform, compute the GST liability, and ensure that payment is made entirely in cash for these transactions. Simultaneously, they must track their own taxable supplies and manage input tax credit utilization accordingly.

The operator must also issue tax invoices in its own name for notified services, even though it is not the actual service provider. This requires robust accounting systems that can segregate transactions and apply the correct tax treatment.

Monthly and annual GST returns must accurately reflect both categories of supplies and the method of payment. Given the volume of transactions many e-commerce platforms handle, automation and strong internal controls are essential to avoid errors.

Importance of Clarity on ITC Treatment

The ability to claim and utilize input tax credit is a cornerstone of the GST framework, helping businesses avoid cascading tax costs. However, the restriction on using ITC for liabilities under Section 9(5) creates a special case for e-commerce operators.

Without clear rules, operators could mistakenly use ITC to offset liabilities that must be paid in cash. This could lead to significant compliance issues, including demands for repayment, interest, and penalties. By clarifying that ITC can be claimed for eligible inputs and services but not used for Section 9(5) liabilities, the government ensures both fairness and compliance consistency.

In practice, this means operators should treat ITC related to notified services as a claimable but non-usable credit for those specific liabilities. That credit can still be applied against the operator’s own service liabilities, which makes careful allocation and tracking essential.

Practical Implications for Platforms with Multiple Service Categories

Many e-commerce platforms operate in multiple service categories, some of which may be notified under Section 9(5) while others are not. For example, a platform could facilitate passenger transport, food delivery, and retail goods sales.

In such cases, the platform’s accounting and GST compliance processes must be capable of distinguishing between:

  • Notified services where liability is payable in cash

  • Own services where liability can be offset with ITC

  • Supplies outside Section 9(5) entirely, which follow standard GST rules

Without proper segregation, the risk of incorrect credit utilization increases. The operator must have clear policies for invoice generation, payment processing, and credit application to ensure compliance across all categories.

Case Examples of Liability Determination

Consider a platform that facilitates both restaurant services and online advertising for those restaurants. The restaurant services are notified under Section 9(5), so the platform must pay GST on the value of those services entirely in cash. The advertising services are the platform’s own taxable supplies, so it can use available ITC to offset the GST liability on those transactions.

In another scenario, a platform provides ride-hailing services and charges drivers a subscription fee for access to premium platform features. The ride-hailing services may be notified under Section 9(5), requiring cash payment for GST, while the subscription fee falls under the platform’s own services, allowing ITC utilization.

These examples illustrate why accurate categorization is critical. Misclassification can lead to the wrong method of payment, triggering compliance issues.

Introduction to Input Tax Credit in the GST Framework

Input tax credit is a mechanism in the Goods and Services Tax system that allows businesses to offset the GST they pay on inputs against the GST they collect on outputs. It ensures that tax is levied only on the value addition at each stage, preventing a cascading effect. For any registered business, availing and utilizing ITC correctly is essential to reduce the effective tax burden.

For e-commerce operators, the situation is more complex because their transactions often include both their own supplies and supplies notified under Section 9(5) where they are deemed to be the supplier. While ITC rules are broadly consistent across sectors, certain specific restrictions apply when dealing with notified services, as clarified by the Central Board of Indirect Taxes and Customs.

Scope of ITC Entitlement for E-Commerce Operators

E-commerce operators can claim input tax credit on goods and services used in the course or furtherance of their business, provided those goods or services are not blocked under Section 17(5) of the CGST Act. This entitlement covers inputs used for facilitating both their own taxable services and the notified services under Section 9(5).

In practical terms, this means that expenses such as software subscriptions for platform management, payment gateway charges, server hosting, and marketing costs may all be eligible for ITC, as long as they are directly connected to the operator’s business activities. The entitlement applies regardless of whether the underlying service is provided directly by the operator or facilitated through third-party service providers.

The entitlement to claim ITC, however, does not automatically mean the operator can use that ITC for every tax liability. This is where the utilization rules become critical, especially in the context of Section 9(5) liabilities.

Special Restriction for Section 9(5) Liabilities

Circular No. 240/34/2024-GST makes it clear that while e-commerce operators can claim ITC for eligible inputs and input services used in providing notified services, they cannot use this credit to pay the GST liability arising under Section 9(5). That liability must be discharged entirely in cash through the electronic cash ledger.

The restriction is rooted in the principle that certain categories of liability under GST must be settled without offsetting through ITC to ensure direct cash payment into the treasury. For operators, this means that even if they have substantial ITC balances, they will need to ensure sufficient cash availability to meet their notified service liabilities.

The cash payment requirement is not unique to Section 9(5), but in this context, it is particularly important because many platforms handle a high volume of notified service transactions. This makes cash flow planning a critical aspect of compliance.

Utilization of ITC for Own Services

While the restriction applies to notified services, e-commerce operators remain free to use ITC for GST liabilities arising from their own services. These services include commissions, facilitation fees, advertising charges, premium listings, and other value-added offerings provided to vendors or customers on the platform.

For these services, the GST liability can be discharged by utilizing available ITC first, and any remaining liability after credit utilization can be paid in cash. This flexibility helps operators optimize their tax payments and reduce the net cash outflow required for their own service liabilities.

An effective compliance system will therefore involve identifying which portion of the ITC pool can be applied against own service liabilities and which portion must effectively be reserved for other uses because it cannot offset Section 9(5) liabilities.

Record-Keeping Requirements for ITC Claims

Accurate record-keeping is fundamental to claiming ITC and using it correctly. Operators must maintain tax invoices or debit notes issued by registered suppliers, payment proofs, and evidence of receipt of goods or services. Under GST law, credits can be claimed only if the supplier has filed the relevant returns and paid the tax to the government.

For operators with both notified services and own services, record-keeping must also include clear allocation of expenses between the two categories. For example, if marketing costs are incurred for both categories, the operator must have a reasonable basis for apportioning those costs for ITC purposes. This helps in ensuring that credit is not misapplied and that returns accurately reflect the correct liabilities.

Illustrative Scenarios of ITC Application

To understand how the rules operate in practice, consider the following examples:

Scenario 1: A platform facilitates online food delivery and charges restaurants a commission. The food delivery service is notified under Section 9(5), and the platform must pay GST on the full value of the delivery orders in cash. However, the commission charged to restaurants is the platform’s own service. ITC can be used to pay GST on that commission.

Scenario 2: A ride-hailing platform provides transportation services and also charges drivers a subscription fee for access to premium features. The transportation service falls under Section 9(5) and its GST liability must be paid in cash, but the subscription fee is a separate taxable service, allowing ITC utilization.

Scenario 3: A platform offers both hotel booking services and advertising space for hotels. If hotel booking is notified under Section 9(5), its liability requires cash payment. The advertising service is the platform’s own supply and can be offset with ITC.

These scenarios highlight why careful categorization is essential. Misapplication of ITC to a Section 9(5) liability would be a compliance error and could attract penalties.

Cash Flow Considerations for Operators

The restriction on ITC utilization for Section 9(5) liabilities creates an additional cash flow management challenge. Operators must ensure they have enough liquidity to meet these liabilities on time, even when they have large ITC balances.

This can require advance planning, especially for platforms with seasonal fluctuations in business volume. For example, during a peak festival season, food delivery orders might surge, leading to higher Section 9(5) liabilities. Without proper planning, the operator might face a cash crunch even though it holds significant unused ITC.

Integrating tax liability forecasting into financial planning helps operators avoid such issues. This may involve setting aside a portion of collected amounts specifically for cash payment of Section 9(5) liabilities, rather than treating all receipts as general revenue.

Compliance Risks of Misutilization

Using ITC incorrectly for Section 9(5) liabilities can lead to serious compliance consequences. The GST authorities can demand repayment of the wrongly utilized credit, along with interest from the date of incorrect utilization. Penalties may also apply if the authorities determine that the misapplication was deliberate or due to gross negligence.

In addition to financial consequences, incorrect ITC utilization can damage a platform’s compliance record. This may lead to more frequent audits or scrutiny in future periods. Given that e-commerce operators are already under close observation due to the high volume of transactions they handle, avoiding such errors is in the operator’s best interest.

Interplay with Section 17 of the CGST Act

Section 17 of the CGST Act deals with apportionment and blocked credits. For e-commerce operators, this section becomes relevant when inputs and services are used partly for taxable supplies and partly for exempt supplies or non-business purposes. Since notified services under Section 9(5) are taxable supplies, the restriction on ITC utilization here does not stem from Section 17 but from specific government clarifications.

However, if an operator also makes exempt supplies, Section 17 rules on proportionate ITC reversal may apply. This adds another layer of complexity in managing ITC, particularly for platforms with a diverse range of service offerings.

Role of Technology in Managing ITC Compliance

Given the transaction volumes and complexity of categorization between notified services and own services, manual management of ITC is impractical for most e-commerce operators. Advanced accounting and ERP systems can be configured to tag each transaction type, allocate credits appropriately, and generate separate liability reports for cash and ITC-eligible payments.

Technology solutions can also help reconcile vendor invoices with GST returns to ensure that ITC is claimed only when the supplier has reported the transaction and paid the tax. Automated reconciliation reduces the risk of claiming ineligible credits, which can otherwise result in reversals and penalties.

Importance of Cross-Functional Coordination

Managing ITC and complying with Section 9(5) rules is not just the responsibility of the finance team. Operations teams need to understand how services are categorized, sales teams must ensure invoices are correctly issued, and legal teams must stay updated on changes to notified services.

Cross-functional communication ensures that the entire organization is aligned on the rules and that no department inadvertently creates a compliance risk. For example, if the marketing team runs a campaign for a new notified service, the finance team must be aware to track and allocate related ITC correctly.

Learning from the Restaurant Services Precedent

The clarifications for restaurant services in the earlier circular provided a clear framework for ITC entitlement and utilization under Section 9(5). Many platforms have since adapted their systems based on that guidance, and the extension of those principles to other notified services allows for consistency in approach.

The key takeaway is that the entitlement to claim ITC does not necessarily mean the credit can be used for every liability. Operators that learned to manage cash payments for restaurant service liabilities are well positioned to apply the same principles to other notified services.

Introduction to Practical Compliance Challenges

E-commerce operators functioning under Section 9(5) of the CGST Act operate in a complex tax environment. Not only do they have to collect, pay, and report taxes for their own services, but they must also discharge the liability for certain notified services as if they were the actual suppliers. This dual role creates operational, accounting, and legal challenges that require structured processes and disciplined execution.

The government’s clarifications on input tax credit entitlement and utilization have removed much of the ambiguity in how operators should handle liabilities. However, the challenge now lies in implementing those clarifications into daily business operations while ensuring accuracy, transparency, and efficiency.

Segregating Transactions by Service Category

The most fundamental strategy for compliance is to maintain a clear segregation of transactions into different service categories. These generally fall into:

  • Notified services under Section 9(5) where GST liability is paid in cash.

  • Own taxable services where ITC can be used to discharge liability.

  • Other taxable supplies or exempt supplies outside Section 9(5).

Segregation at the transaction level ensures that invoicing, accounting, and tax payment processes remain accurate. For example, ride-hailing transactions must be tagged as Section 9(5) services, while advertising fees charged to drivers should be tagged as their own services. This separation allows for precise computation of liabilities and prevents accidental ITC utilization for restricted categories.

Designing Accounting Systems for Compliance

To manage the complexities of Section 9(5) compliance, operators should invest in accounting and ERP systems that are capable of:

  • Tagging each transaction with the correct service classification.

  • Automating the allocation of ITC only to eligible liabilities.

  • Generating reports on cash liabilities for notified services.

  • Reconciling input tax credits with supplier returns.

Such systems should also be able to integrate with GST return filing tools, reducing manual intervention and the risk of errors. Given the volume of transactions for most e-commerce platforms, automation is not just a convenience but a necessity for maintaining compliance.

Implementing Cash Flow Management for Notified Service Liabilities

Because liabilities for notified services must be paid entirely in cash, e-commerce operators need robust cash flow management strategies. This begins with forecasting expected liabilities based on historical transaction volumes and seasonal demand patterns.

Setting aside a portion of the collections specifically for these liabilities helps avoid last-minute cash shortages. Some operators establish dedicated bank accounts for tax liabilities to prevent operational funds from being used for other purposes. Others implement daily or weekly transfers to their electronic cash ledger to spread the impact of large monthly payments.

Maintaining Comprehensive Documentation

Documentation plays a vital role in supporting ITC claims and demonstrating compliance during audits. E-commerce operators should maintain:

  • Tax invoices and debit notes for all purchases.

  • Proof of payment to suppliers.

  • Records of goods or services received.

  • Internal reports showing allocation of ITC between different service categories.

  • Monthly reconciliations between supplier filings and claimed credits.

For notified services, records should also clearly show the calculation of liabilities and evidence of cash payment through the electronic cash ledger. Proper documentation ensures that if the authorities question any transaction, the operator can provide evidence to substantiate the compliance position.

Training and Awareness Across Departments

Compliance with Section 9(5) rules is not limited to the finance team. Sales, marketing, operations, and technology departments all play a role in ensuring the business remains compliant. Training programs should be conducted to educate relevant staff about:

  • Which services are notified under Section 9(5).

  • How liabilities for those services are calculated.

  • Restrictions on ITC utilization for certain liabilities.

  • Importance of accurate data entry and transaction tagging.

This cross-departmental awareness helps prevent situations where, for example, marketing campaigns misclassify a service or the operations team inputs incorrect tax codes into the system.

Leveraging the Precedent from Restaurant Services

The earlier experience with restaurant services under Section 9(5) offers valuable lessons. Platforms that had to adjust their systems to handle cash-only payments for those services now have a template for managing similar requirements in other notified services. The key strategies that emerged from that experience include:

  • Creating separate tax ledgers for different service categories.

  • Implementing automatic alerts when cash ledger balances are running low.

  • Conducting regular internal audits to confirm that ITC utilization rules are being followed.

By applying these proven methods, operators can reduce the learning curve and implement compliant processes more quickly.

Periodic Internal Audits for Risk Mitigation

Regular internal audits help identify and correct compliance issues before they escalate into penalties. These audits should include:

  • Reviewing transaction classifications.

  • Checking that ITC has been utilized only for eligible liabilities.

  • Verifying cash payments for Section 9(5) liabilities.

  • Reconciling ITC claims with supplier filings in the GST portal.

Audits can be conducted monthly or quarterly depending on the volume of transactions. The findings should be documented, and corrective measures should be implemented promptly.

Using Technology for GST Reconciliation

Technology-driven reconciliation tools can match purchase invoices with supplier filings in real time. This ensures that ITC is claimed only when the supplier has reported the transaction and paid the tax. 

Given the dynamic nature of e-commerce transactions, automated reconciliation helps maintain accuracy without overwhelming the finance team. Reconciliation tools can also integrate with ERP systems to automatically adjust ITC claims when discrepancies are found, ensuring that returns are always in line with legal requirements.

Coordinating with Suppliers for Timely Compliance

Since ITC can only be claimed when the supplier has complied with filing and payment obligations, e-commerce operators should actively coordinate with their suppliers. This can involve:

  • Sending reminders to suppliers to file returns on time.

  • Conducting supplier compliance checks before onboarding.

  • Including GST compliance clauses in contracts.

By working closely with suppliers, operators can reduce the risk of ITC reversals and maintain accurate credit balances.

Preparing for GST Audits and Departmental Inquiries

GST audits and inquiries can be triggered by discrepancies in returns, random selection, or targeted risk assessment by the tax authorities. E-commerce operators should be prepared with:

  • A clear explanation of how Section 9(5) liabilities are calculated.

  • Evidence of segregation between notified and own services.

  • Documentation supporting ITC claims and utilization.

  • System reports showing compliance with cash payment requirements.

Proactive preparation not only reduces the stress of an audit but also demonstrates the operator’s commitment to compliance, which can influence the outcome of the inquiry.

Monitoring Changes in Notified Services List

The list of services notified under Section 9(5) is not static. The government may add new services or remove existing ones based on evolving policy needs. E-commerce operators must monitor official notifications and circulars regularly to stay updated.

A sudden inclusion of a service in the notified list can have significant operational and cash flow implications. Platforms should have contingency plans for quickly updating systems, retraining staff, and adjusting financial forecasts when such changes occur.

Building a Compliance Calendar

A compliance calendar helps operators track all GST-related deadlines, including return filing dates, payment due dates, and reconciliation schedules. This calendar should also include reminders for:

  • Internal audit cycles.

  • Supplier compliance reviews.

  • Staff training sessions.

  • Updates from government notifications.

Having a centralized calendar reduces the risk of missed deadlines, which can result in penalties or interest charges.

Communicating Compliance Efforts to Stakeholders

For large e-commerce operators, compliance with Section 9(5) is not only a legal requirement but also a matter of business credibility. Communicating compliance measures to investors, partners, and customers can build trust and confidence.

This can be done through periodic updates in internal reports, annual disclosures, or even targeted communications to partners who rely on the platform for their business. A reputation for strong compliance can also make it easier to work with larger corporate clients who value regulatory stability.

Planning for System Scalability

As e-commerce platforms grow, the volume of transactions under Section 9(5) can increase substantially. Systems and processes that work for smaller volumes may not scale effectively. Operators should plan for scalability by:

  • Choosing ERP systems that can handle higher transaction volumes.

  • Automating more compliance functions as the business grows.

  • Reviewing staffing needs in the finance and compliance teams.

Scalability planning ensures that growth does not lead to compliance failures.

Integrating Compliance into Business Strategy

For e-commerce operators, compliance with Section 9(5) should not be treated as an afterthought or purely administrative task. It should be integrated into the broader business strategy. 

This means that when new services are launched or partnerships are formed, the potential GST implications under Section 9(5) are assessed early in the decision-making process. By incorporating compliance into strategy, operators can avoid costly rework and ensure that new initiatives align with legal requirements from the outset.

Conclusion

E-commerce operators under Section 9(5) of the CGST Act work within a unique compliance framework that blends their role as facilitators of third-party services with their responsibilities as direct taxpayers for notified supplies. The government’s clarifications, particularly through Circular No. 240/34/2024-GST, have brought greater certainty to how input tax credit can be claimed and utilized in this context, while reinforcing the requirement that liabilities for notified services must be paid entirely in cash.

Successfully managing these obligations requires more than just awareness of the law. It demands robust systems to segregate transactions, meticulous record-keeping, disciplined cash flow planning, and a strong culture of compliance across all departments. Leveraging lessons from earlier applications of Section 9(5), such as the treatment of restaurant services, allows operators to adapt proven strategies to new service categories as they are notified.

With the right combination of technology, processes, and proactive monitoring of regulatory changes, e-commerce operators can maintain full compliance while optimizing their use of input tax credit for eligible liabilities. This not only minimizes the risk of penalties and interest but also strengthens operational resilience and builds trust with stakeholders in an increasingly regulated digital marketplace.