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Issues Faced while Filing GSTR 9 and GSTR 9C

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  • Post published:October 10, 2023
  • Post category:GST Return


Last Updated on October 10, 2023 by Maria

Goods and Services Tax (GST) has significantly transformed India’s taxation system, making it more streamlined and transparent. As part of the GST regime, businesses must file various returns to accurately report their financial activities and tax liabilities. Two crucial annual return forms under GST are GSTR 9 and GSTR 9C.

GSTR 9, the Annual Return, is a comprehensive summary of a taxpayer’s GST transactions for a particular financial year. On the other hand, GSTR 9C is the GST Audit Report, a document that ensures the accuracy of the annual returns filed in GSTR 9 by conducting a thorough audit.

This article will explore the intricacies of GSTR 9 and GSTR 9C, exploring their significance in the GST ecosystem. We will discuss the entities obligated to file these returns, their due dates, and penalties for non-compliance. Additionally, we will address the common challenges and issues taxpayers face during the filing process and provide valuable insights into best practices for successful compliance. Understanding and effectively managing GSTR 9 and GSTR 9C is essential for businesses to maintain smooth GST operations and avoid penalties.

Overview of GSTR 9

GSTR 9, the Annual Return under the Goods and Services Tax (GST) regime, is vital for businesses to consolidate their entire year’s financial activities and tax information. This return provides a comprehensive summary of all the GST transactions conducted during a specific financial year, ensuring transparency and compliance with GST regulations.

Entities registered under GST, including regular taxpayers, composition scheme dealers, and e-commerce operators, must file GSTR 9. It is a statutory obligation that allows businesses to report their income, input tax credits, and tax liability for the entire fiscal year.

The due date for filing GSTR 9 is typically on or before December 31st of the subsequent financial year. Timely compliance is crucial to avoid penalties and legal consequences. Failure to file GSTR 9 within the stipulated time frame can result in penalties, including fines and interest charges, which can adversely affect a business’s financial health.

Overview of GSTR 9C 

GSTR 9C is a critical component of GST compliance that ensures the accuracy and integrity of the financial information provided in GSTR 9. It serves as the audit or reconciliation statement, enhancing transparency and accountability in the GST reporting process.

While GSTR 9 provides a summary of annual GST transactions, GSTR 9C is the audit mechanism that validates the accuracy of these transactions. The audit is conducted by a qualified chartered accountant or cost accountant who verifies whether the financial statements presented in GSTR 9 fairly represent the business’s actual transactions and financial position.

Under GST law, GSTR 9C is mandatory for certain categories of taxpayers, specifically those whose aggregate turnover exceeds a prescribed threshold. For large businesses, this audit is a legal requirement and a crucial practice to maintain financial credibility and compliance.

Common Issues in GSTR 9 Filing

  • Data Reconciliation: One of the primary issues faced during GSTR 9 filing is the reconciliation of data between different GST returns, particularly GSTR 1 and GSTR 3B. Mismatched data can lead to discrepancies and notices from tax authorities. To overcome this challenge, businesses should maintain accurate records and regularly reconcile their data. Employing accounting software that integrates with the GST portal can streamline this process.
  • Input Tax Credit (ITC) Reconciliation: Reconciling ITC is another significant hurdle. Many taxpayers struggle to match the ITC claimed in GSTR 3B with the eligible ITC available per their purchase records. This can result in ITC reversals and additional tax liabilities. To address this, businesses should maintain a robust mechanism to track and verify ITC at every stage. Regularly reconciling purchase registers with GSTR 2A can help identify discrepancies early on.
  • Amendment of Errors: Correcting errors or making amendments in GSTR 9 can be challenging. Some taxpayers may not know the correct procedure for rectifying mistakes made in previous returns. To mitigate this issue, it’s essential to maintain thorough documentation of all transactions and amendments. Consultation with tax professionals or GST experts can also guide the correct amendment procedure.
  • ITC on Exempt Supplies: Calculating ITC on exempt supplies is another complex issue. Businesses need to differentiate between inputs used for taxable and exempt supplies accurately. Implementing a system that categorizes inputs based on their end use can simplify this process.
  • Reversal of ITC: Reversing ITC under various scenarios, such as non-payment to suppliers within 180 days, can be tricky. Businesses should closely monitor the status of vendor payments and ensure compliance with GST provisions to avoid ITC reversals.

Common Issues in GSTR 9C Audit

  • Incomplete or Inaccurate Documentation: One of the most common issues is the absence of complete and accurate documentation. Auditors often face challenges when they encounter missing invoices, mismatched records, or inadequate supporting documents. To mitigate this, taxpayers should maintain meticulous records of all transactions, including invoices, purchase orders, and payment receipts.
  • Tax Liability Reconciliation: Reconciling the tax liability reported in GSTR 3B with the audited financial statements can be complex. Discrepancies between the two can result in additional tax liabilities. Taxpayers should regularly reconcile their GST data with their financial records to identify and rectify inconsistencies promptly.
  • Certifications and Compliance: The auditor’s certification is crucial in GSTR 9C. Many businesses struggle to meet all the necessary compliance requirements, leading to issues with certification. Taxpayers should adhere to GST regulations and maintain a robust compliance framework to address this.
  • Complex Business Structures: For businesses with complex structures or multiple business verticals, allocation and reconciliation of data can be challenging. It’s essential to segregate and document transactions correctly for each vertical to simplify the audit process.
  • ITC Verification: Auditors scrutinize Input Tax Credit (ITC) claims thoroughly. Ensuring that ITC claims align with the supporting documents is crucial. Regularly reconciling purchase registers with GSTR 2A and addressing any mismatches can help avoid ITC-related issues.
  • Amendment and Rectification: Correcting errors identified during the audit can be cumbersome if not handled correctly. Taxpayers should be aware of the procedure for making amendments and rectifications in the audit report to avoid compliance issues.

Impact of Late or Incorrect Filing 

  1. Penalties: Late filing of GSTR 9 and GSTR 9C invites financial penalties. The penalty for failing to file GSTR 9 within the due date is typically ₹100 per day of delay, subject to a maximum of 0.25% of the taxpayer’s turnover. For GSTR 9C, the penalty for late filing can be up to ₹200 per day of delay.
  2. Interest: Delayed payment of GST liabilities or incorrect reporting can lead to the imposition of interest. The interest rate is generally 18% per annum, calculated from the due date until the actual payment date.
  3. Legal Implications: Persistent non-compliance or substantial discrepancies in filings can attract legal action. Authorities may initiate investigations or audits, which can be time-consuming and may result in further penalties and fines.
  4. Reconciliation Issues: Incorrect filing can lead to discrepancies in data, causing reconciliation challenges. These discrepancies can lead to disagreements with tax authorities and additional scrutiny.

Best Practices for GSTR 9 and GSTR 9C 

  1. Maintain Accurate Records: Keep meticulous records of all financial transactions, including invoices, expenses, and input tax credit details. Accurate records are the foundation of successful GST compliance.
  2. Regular Reconciliation: Perform regular reconciliations of your data to identify discrepancies promptly. This proactive approach can prevent last-minute challenges during filing.
  3. Seek Professional Guidance: Engage with GST experts or chartered accountants specialising in GST compliance. Their expertise can help navigate complex rules and ensure accurate filings.
  4. Timely Data Entry: Ensure data is entered accurately and promptly into your accounting software. Timely data entry can prevent issues caused by backlog.
  5. Training and Awareness: Train your finance and accounting teams on the latest GST rules and updates. Staying informed about changes in GST regulations is crucial.
  6. Periodic Review: Conduct periodic internal reviews of your financial data and GST filings to identify potential discrepancies or issues.
  7. Documentation: Maintain well-organized documentation of all transactions, including invoices, bills of supply, and input tax credit records. Organized documentation simplifies the audit process.
  8. Regular Communication: Maintain open communication with your GST consultant or auditor. Discuss any concerns or issues as they arise to address them promptly.
  9. Proactive Compliance: Proactively comply with GST regulations before the filing deadline. This approach can prevent last-minute rush and errors.

Recent Changes and Updates 

  1. Relaxation in Late Fees: In response to the COVID-19 pandemic, authorities have provided relief by reducing or waiving late fees for delayed filings. However, these relaxations may change, so it is crucial to check the latest notifications.
  2. Extension of Due Dates: Due dates for filing GSTR 9 and GSTR 9C have been extended in certain cases to accommodate the challenges faced during the pandemic. Taxpayers should be aware of these extended deadlines to avoid penalties.
  3. QRMP Scheme: The Quarterly Return Monthly Payment (QRMP) scheme allows small taxpayers to file GSTR 1 and GSTR 3B quarterly. Taxpayers opting for this scheme must understand its implications on GSTR 9 and GSTR 9C filings.
  4. Digital Signature: Using digital signatures for GSTR 9C filing has become mandatory for certain taxpayers. It’s crucial to be aware of this requirement and ensure compliance.
  5. E-Invoicing: The introduction of e-invoicing has impacted the reporting of B2B transactions. Taxpayers must adapt their processes to correctly incorporate e-invoicing data into GSTR 9 and GSTR 9C.
  6. Annual Aggregate Turnover: Changes in the definition of aggregate turnover can affect whether a taxpayer must file GSTR 9 or GSTR 9C. Ensure that your business’s turnover aligns with the latest criteria.

Tips for Successful GSTR 9 and GSTR 9C Filing 

  1. Maintain Organized Records: Keep meticulous records of all your financial transactions, invoices, and relevant documents. This will make the filing process smoother and reduce the chances of errors.
  2. Regular Reconciliation: Reconcile your data periodically to identify and rectify discrepancies promptly. This practice will save you time during the filing process and minimize non-compliance risk.
  3. Seek Professional Help: Consider engaging tax professionals or consultants who specialize in GST. Their expertise can help you navigate complex rules, stay updated with changes, and ensure accurate filings.
  4. Stay Informed: Regularly check for GST updates, amendments, and notifications. Government guidelines can change, and staying informed is crucial to compliance.
  5. Invest in Software: Explore GST software solutions that can automate data entry and reconciliation. These tools can significantly reduce the risk of errors.
  6. Conduct Mock Audits: Simulate GSTR 9C audits internally to identify potential issues. This will help you address problems proactively.
  7. Learn from Past Mistakes: If you have faced challenges in previous filings, learn from those experiences and improve your compliance process.
  8. Engage in Training: Invest in training and workshops for your finance and accounting teams to keep them updated with GST regulations and procedures.
  9. Stay Proactive: Lastly, be proactive in your compliance efforts. GST rules are subject to change, and proactive adaptation is key to avoiding penalties.


Filing GSTR 9 and GSTR 9C is a critical aspect of GST compliance for businesses in India. While these annual returns and audits can be complex and challenging, careful planning, attention to detail, and proactive measures can make the process smoother.

Avoiding common issues, staying informed about updates, and seeking professional assistance when necessary are essential steps toward successful compliance. Remember that timely and accurate filing not only ensures compliance with the law but also contributes to your business’s overall financial health and reputation.

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