Summary
CBIC Clarification on Late Fee for Delayed Filing of GSTR-9C
The Central Board of Indirect Taxes and Customs (CBIC), through Circular No. 246/03/2025-GST dated 30 January 2025, clarified the applicability and calculation of late fee where a registered person files FORM GSTR-9C after filing FORM GSTR-9.
The clarification concerns Section 47(2) and Section 44 of the CGST Act, 2017, read with Rule 80 of the CGST Rules, 2017.
1. When Is GSTR-9C Required?
Under the provisions explained in the circular, registered persons whose aggregate turnover exceeds the prescribed threshold are required to furnish a reconciliation statement in FORM GSTR-9C along with the annual return in FORM GSTR-9.
For financial years from 1 August 2021 onwards, the circular refers to the requirement for taxpayers having aggregate turnover exceeding ₹5 crore during the financial year to furnish a self-certified reconciliation statement in FORM GSTR-9C.
The applicable threshold and filing requirements should be checked for the relevant financial year.
2. Is Late Fee Payable If GSTR-9C Is Filed After GSTR-9?
CBIC has clarified that where GSTR-9C is required, the annual return under Section 44 is not complete until both FORM GSTR-9 and FORM GSTR-9C have been furnished.
Therefore, filing GSTR-9 alone does not complete the annual return where GSTR-9C is also mandatory.
Late fee under Section 47(2) is calculated from the due date of the annual return until the date on which the complete annual return is furnished.
3. How Is the Late Fee Period Determined?
The circular clarifies the following situations:
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GSTR-9C is not required: The relevant date for completion of the annual return is the date on which GSTR-9 is filed.
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GSTR-9C is required and filed along with GSTR-9: The relevant date is the date on which the two forms are furnished as a complete annual return.
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GSTR-9C is required but filed later: The relevant date is the date on which GSTR-9C is subsequently furnished, completing the annual return.
Late fee is not calculated as two separate late fees for GSTR-9 and GSTR-9C. It is calculated for the delay in furnishing the complete annual return, subject to the applicable statutory limits and relief.
4. Conditional Late Fee Waiver for Financial Years up to FY 2022-23
The circular also refers to Notification No. 08/2025-Central Tax dated 23 January 2025, which provides a conditional waiver of the specified excess late fee for delayed filing of the complete annual return for financial years up to FY 2022-23.
The relief applies where the required FORM GSTR-9C is furnished on or before 31 March 2025, subject to the terms of the notification.
In such cases, no additional late fee is payable for the delayed filing of GSTR-9C to the extent covered by the waiver described in the circular. However, the circular clarifies that any late fee already paid for delayed furnishing of GSTR-9C for those financial years is not refundable under this provision.
The deadline stated in this circular was 31 March 2025. Taxpayers should verify the applicable notification and any subsequent legal developments before relying on this historical waiver.
5. Practical Implications for Taxpayers
Taxpayers reviewing their annual return compliance should check:
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Whether GSTR-9C was mandatory for the relevant financial year.
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The due date applicable to the annual return.
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The actual filing dates of GSTR-9 and GSTR-9C.
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The late fee calculation up to the date of completion of the annual return.
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Whether any specific waiver notification applies to the relevant financial year.
Official Reference
CBIC Circular No. 246/03/2025-GST dated 30 January 2025.
Related notification: Notification No. 08/2025-Central Tax dated 23 January 2025.
Need Assistance with GST Annual Return or Late Fee Issues?
If you have received a late fee demand or need to review delayed GSTR-9 or GSTR-9C filing, an examination of the applicable financial year, turnover, filing dates and relevant notifications may help determine the correct position.
Contact Taxation360 for professional assistance.
Disclaimer: This article is for general informational purposes only and does not constitute case-specific legal advice.