GSTR-9C Reconciliation Statement: Who Needs It and What It Compares

GSTR-9C is a reconciliation statement that goes with your GST annual return. You need it only if your aggregate turnover in the financial year is above Rs 5 crore. It compares the figures in your audited accounts with the figures in GSTR-9, and you certify it yourself. For FY 2025-26 it is due by 31 December 2026.

What is GSTR-9C, and why does it exist?

Your annual return in GSTR-9 adds up what you told the GST portal during the year. Your audited accounts add up what actually happened in the business. GSTR-9C puts the two side by side and makes you account for every rupee of difference.

Why only for larger businesses? Because reconciliation takes real work, and the government decided the effort is worth asking for only above Rs 5 crore. For a business of that size, a 1% gap is Rs 5 lakh of turnover, which is worth explaining.

Who needs to file it?

Every regular registered person whose aggregate turnover in the financial year is more than Rs 5 crore. Aggregate turnover means all supplies under one PAN across India: taxable, exempt and export, without the GST itself.

Two points trip people up.

• The Rs 5 crore test is on the PAN. The statement is filed for each GSTIN. A company with Rs 3 crore in Gujarat and Rs 4 crore in Maharashtra files two GSTR-9C, one for each State.
• Input service distributors, casual and non-resident taxable persons, and persons who only deduct TDS or collect TCS under GST do not file it.

Up to Rs 5 crore, you stop at GSTR-9, and up to Rs 2 crore you are exempt from that as well.

Do you still need a CA to certify it?

No. Until FY 2019-20, accounts had to be audited under the GST law above Rs 2 crore, and a chartered accountant or cost accountant certified GSTR-9C. Notification 30/2021-Central Tax replaced Rule 80 from 1 August 2021. Since then the rule asks for a self-certified statement above Rs 5 crore, starting with the statement for FY 2020-21.

Self-certified does not mean casual. You sign that the figures are true. Most businesses of this size still have the working prepared by whoever audits their accounts, because the numbers must tie to the audited balance sheet.

What are the parts of GSTR-9C?

The form ends with your verification. Where should you spend your time? On Tables 5 and 12. If turnover and credit reconcile, the rest follows.

What differences usually need explaining?

• Timing. Revenue booked in March but invoiced in April, or advances received on which GST was paid before the sale was booked.
• Items in the accounts that are not supplies. Interest income, dividends, foreign exchange gains, discounts received.
• Supplies that are not in the accounts as sales. Stock transfers between your own GSTINs, sale of old assets, free samples on which tax was paid.
• Credit notes. Issued in the books but reported late, or not accepted for GST.
• Multi-State split. One set of accounts for the company, divided across GSTINs.
• Credit. Credit booked in one year and claimed in the next, blocked credit that sits in expenses, reversals for exempt sales.

A difference with a reason is fine. A difference without one becomes tax payable in Part V.

A worked example

Your company has one GSTIN. The audited accounts for FY 2025-26 show sales of Rs 8,40,00,000. GSTR-9 shows Rs 8,31,00,000. The gap is Rs 9,00,000.

• Rs 6,00,000 is work completed in March 2026 and booked as revenue, but invoiced in April 2026. It will appear in next year's returns. Explained.
• Rs 3,00,000 is a January 2026 invoice that is in the books but was never reported in GSTR-1 or GSTR-3B. Not explained. Tax at 18% is Rs 54,000.

You pay the Rs 54,000 through Form DRC-03, the voluntary payment form, on 15 December 2026. The January return was due on 20 February 2026, so interest runs for 298 days: Rs 54,000 x 18% x 298/365 = Rs 7,936. Total: Rs 61,936.

Now suppose you file GSTR-9 on 28 December 2026 but GSTR-9C only on 20 January 2027. The annual return is complete on 20 January, 20 days late. At Rs 100 a day for turnover between Rs 5 crore and Rs 20 crore, the late fee is Rs 2,000. The cap is 0.04% of turnover in the State, Rs 33,600 here.

What is the due date and the late fee position?

Rule 80(3) asks for GSTR-9C along with GSTR-9, on or before 31 December after the financial year. For years there was doubt over whether a late GSTR-9C alone attracted late fee. Circular 246/03/2025-GST, dated 30 January 2025, settled it.

• Where GSTR-9C is required, the annual return is complete only when both forms are filed.
• Late fee under section 47(2) runs from the due date to the date the later of the two is filed.
• It is not charged twice. The portal collects the GSTR-9 part with GSTR-9 and the remaining days in Table 17 of GSTR-9C.

The daily rate and cap are the same as for GSTR-9: Rs 50 a day up to Rs 5 crore turnover, Rs 100 a day up to Rs 20 crore and Rs 200 a day above that, counting CGST and SGST together. A GSTR-9C filer is always in the second or third slab.

For old years there was a one-time relief. Notification 08/2025-Central Tax waived the extra late fee for GSTR-9C of any year up to FY 2022-23, if the statement was filed by 31 March 2025. That window has closed.

The mistake people usually make

They file GSTR-9 on 30 December, feel done, and leave GSTR-9C for January because the audit is still open. The fee keeps running on the whole annual return. Worse, a filed GSTR-9 cannot be revised, so anything the reconciliation finds later has to be explained in GSTR-9C instead of corrected in GSTR-9.

Do it the other way round. Finish the reconciliation first, then prepare GSTR-9 from the reconciled figures, then file both together. Our guide on how to file GSTR-9 walks through the annual return itself.

Should you prepare GSTR-9C yourself? If you have an accounts team and one GSTIN, it is manageable. With several GSTINs or large credit differences, involve your auditor early.

Frequently asked questions

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