Late fee on GSTR-9 and GSTR-9C, year by year and turnover by turnover

The statutory fee

Section 47(2) charges a registered person who fails to furnish the annual return under Section 44 by the due date ₹100 for every day of default, subject to a maximum of 0.25% of turnover in the State or Union territory. The same amount is charged under the State or UT Act, so the usual combined figures are ₹200 a day and 0.5% of State turnover.

That full statutory rate still applies to FY 2017-18 to FY 2021-22, subject to the 2023 amnesty below.

From FY 2022-23: by turnover

Notification No. 07/2023-Central Tax reduced the fee for returns from FY 2022-23 onward, by aggregate turnover in the year:

The cap is on turnover in the State or Union territory for the GSTIN, not aggregate turnover. For most small and medium registrations the 0.04% cap is reached quickly, so the fee is usually the cap rather than the daily amount.

Worked example. FY 2023-24, aggregate turnover ₹3 crore, State turnover ₹3 crore, return due 31.12.2024 and filed 15.03.2025 (74 days late). Per Act: ₹25 × 74 = ₹1,850, below the cap of 0.02% × ₹3 crore = ₹6,000. Combined: ₹3,700.

The 2023 amnesty for the older years

For FY 2017-18 to FY 2021-22, the same notification capped the fee at ₹10,000 per Act (₹20,000 combined) where the annual return was filed between 1 April 2023 and 30 June 2023, a window later extended to 31 August 2023 by Notification No. 25/2023-Central Tax. The amnesty depended on the filing date, so a return for one of those years filed after 31 August 2023 is back at the statutory fee.

GSTR-9C: the fee runs until both are filed

Where turnover requires a reconciliation statement in GSTR-9C, Circular No. 246/03/2025-GST (30 January 2025) clarified that the annual return under Section 44 is not furnished until both GSTR-9 and GSTR-9C are furnished. The late fee therefore runs from the due date to the date the later of the two is filed. It is one fee for the complete return, not two fees.

The portal computes the fee when GSTR-9 is filed and not when GSTR-9C follows, so any fee for the gap between the two has to be computed and paid separately, or will be raised by the officer.

Relief for the older years. Notification No. 08/2025-Central Tax (23 January 2025) waived, for any year up to FY 2022-23, the fee beyond what was payable up to the GSTR-9 filing date, provided GSTR-9C was filed by 31 March 2025. A fee already paid is not refunded. For FY 2023-24 onward, and for older years where GSTR-9C came after 31 March 2025, the fee runs to the GSTR-9C date.

For the working paper

Officer:

• For each year, take the due date of GSTR-9, the GSTR-9 filing date and, where required, the GSTR-9C filing date. The fee runs to the later filing date, subject to the 2025 relief.
• Use aggregate turnover for the band and turnover in the State for the cap.
• For FY 2017-18 to 2021-22, check whether the filing fell within the amnesty window of 01.04.2023 to 31.08.2023.
• Desktop check A6 computes the fee from the filed returns for review.

Practitioner:

• File GSTR-9C with GSTR-9. A reconciliation filed later extends the late fee for FY 2023-24 onward.
• Where the portal has charged the fee only to the GSTR-9 date, work out any balance for the gap and pay it, or record why the 2025 relief applies.

The GSTR-9 late fee calculator applies these rules, including the amnesty and the GSTR-9C relief, and the late fee reference sets out the notification trail.