GSTR-9 Filing: Common Mistakes to Avoid While Filing GSTR-9

GSTR-9 is an annual GST return required to be filed by all registered taxpayers, including the SEZ units or SEZ developers, and even those who have opted out of the composition scheme, if their annual turnover is more than Rs 2 crore. If you are someone preparing to file it, read these important points mentioned below to avoid any common mistakes while filing GSTR-9.

Not Filing GSTR-9 If Your Turnover is Below Rs 2 Crore

Filing GSTR-9 is optional if your turnover for the financial year is less than Rs 2 crore. However, the system then generates a draft auto-filled return. If you do not file your GSTR-9, the government will consider this draft return as your final return. Therefore, if you made any corrections during FY 2024-25 or adjusted previous-year data, it is advised to file GSTR-9.

Wrong HSN-Wise Summary

Reporting the correct HSN (Harmonised System of Nomenclature) is important for your GSTR-9 filing. Table 17 requires HSN-wise reporting of outward supplies. If your turnover is up to Rs 5 crore, you must report 4-digit HSN for B2B supplies. If your turnover is more than Rs 5 crore, report 6 or 8-digit HSN for both B2B and B2C. Tables 15, 16, and 18 are optional, so you can skip them unless they are relevant for your filing. Also, you can download your HSN details from Table 12 of GSTR-1.

Always Reconcile Data with GSTR-1

The values auto-filled in Table 4 are based on the GSTR-1 data. Many taxpayers accept this auto-filled data, but sometimes this data can have mistakes. Therefore, always reconcile your data of GSTR-1 with your books or accounts, and GSTR-1 and GSTR-3B. After reconciling the data, use the corrected values as GSTR-9 cannot be revised later.

Incorrect ITC Breakup

In Table 6, businesses are required to give an ITC breakup, which includes inputs, input services, and capital goods. Many businesses fail to break their ITC into these sections, which can result in incorrect returns. Also, if you are eligible to claim ITC on the Reverse Charge Mechanism (RCM), you should have a separate breakup for it. You can also make reconciliation in Excel, month-wise for both sales and ITC.

Not Filing Separate Return for Different Branches

If you have multiple GST registrations for different states or branches under the same PAN, you are required to file GSTR-9 for each GSTIN separately. For example, if one of your branches has a turnover of Rs 10 crore and another has Rs 2 crore, you must file GSTR-9 for both, as the total turnover of both branches is more than Rs 2 crore.

Not Paying Tax Difference in Table 9

In Table 9, if your payable tax changes after calculations. So, you must pay the difference through the Form DRC-03. Now, you can pay this difference through cash or credit ledger. If you do not pay this difference, the department may issue notices, and you might be required to pay this amount along with interest at 18%.

Failing to Report the Correct Data for the Previous Year

If you have any corrections from the previous year, make sure you report them correctly. Tables 10 to 11 are for sales reported. Tables 12 and 13 are for ITC claims. If you add values in Tables 12 or 13, make sure these values also appear in Table 8C.

Forgetting to Report Exempt Sale

Many businesses usually ignore Table 5, but it is mandatory for cases where the recipient pays tax under RCM, or exports made without payment of tax, or for NIL-rated or non-GST supplies such as petroleum products.

Ignoring ITC reconciliation

Many businesses fail to reconcile their Input Tax Credit (ITC). The ITC that gets auto-filled in Table 8A of GSTR-9 is based on GSTR-2B. Taxpayers must note that GSTR-2B is the correct base for ITC claims. Many businesses still use 2A, which is incorrect. So make sure your ITC matches with 2B data, not 2A.

Do Not Delay in Filing

The due date to file GSTR-9 is December 31, 2025. Many businesses wait until the last minute to file their return, which can result in last-minute errors, and the portal may also slow down. Therefore, do not wait for the last day to file GSTR-9. File your return at least 8 to 10 days before the due date so that you have enough time to fix any issues.