CBIC Clarifies Late Fee Rules for GSTR-9C Filing

GST Cir. No. 246: CBIC Issues Clarification on Late Fees for Delayed Filing of GSTR-9C

The Central Board of Indirect Taxes and Customs (CBIC) clarified the application of late fees for failure to file the reconciliation statement in FORM GSTR-9C and the annual return in FORM GSTR-9 on January 30, 2025, with Circular No. 246/03/2025-GST.

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Key Takeaways from the Circular

Late Fee Applicability
- If there are delays in providing both FORM GSTR-9 and GSTR-9C, as applicable, late fees under Section 47(2) of the CGST Act, 2017 would be charged.
- The late charge will be charged from the due date till FORM GSTR-9C is submitted if only FORM GSTR-9 is filed on time but FORM GSTR-9C is not.
Applicability of GSTR-9C Filing
- Businesses with a turnover of more than ₹2 crore had to provide an audited reconciliation statement (GSTR-9C) earlier than August 1, 2021.
- The threshold was raised to ₹5 crore after August 1, 2021, and GSTR-9C was self-certified rather than subject to a statutory audit.
Waiver of Additional Late Fees for Past Financial Years
- Delays in submitting GSTR-9C for the financial years up to FY 2022–2023 are covered by Notification No. 08/2025-Central Tax (dated January 23, 2025).
- No late fees beyond the penalty for submitting FORM GSTR-9 will be assessed if GSTR-9C is filed by March 31, 2025.
- However, late costs that have already been paid will not be refunded.

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Below is a mention of the official circular’s text.

Representations have been received seeking clarification regarding levy of late fee payable for delay in furnishing of reconciliation statement in FORM GSTR-9C. It has been asked if there will be a late fee under section 47 of the Central Goods and Services Tax Act, 2017 (henceforth referred to as the “CGST Act”) in cases where the registered person fails to provide the reconciliation statement in FORM GSTR-9C with the annual return in FORM GSTR-9 but files it after the deadline for providing the annual return.
In the exercise of its authority granted by sub-section (1) of section 168 of the CGST Act, the Board hereby explains the following matters to guarantee consistency in the application of the law amongst the field formations.

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A registered person who is required to have his accounts audited in accordance with the provisions of sub-section (5) of section 35 of the CGST Act must submit the annual return under sub-section (1) of the aforementioned section, together with a copy of the audited annual accounts and a reconciliation statement, according to sub-section (2) of section 44 of the CGST Act prior to August 1, 2021. From August 1, 2021, onwards, sub-section (1) of section 44 of the CGST Act provides for the filing of an annual return, which may include a self-certified reconciliation statement, that reconciles the value of supplies declared in the return furnished for the financial year with the audited annual financial statement for every financial year electronically, within the time, in the form, and in the manner that may be prescribed. This eliminates the need to have accounts audited in accordance with the provisions of sub-section (5) of section 35 of the CGST Act. Additionally, before to August 1, 2021, under subrule (3) of rule 80 of the Central Goods and Services Tax Regulations, if a registered person’s total turnover in a fiscal year exceeds two crore rupees, their accounts will be audited in accordance with sub-section (5) of section 35 of the CGST Act. The taxpayer is required to provide a copy of the audited annual accounts and a duly certified reconciliation statement in FORM GSTR-9C. Subrule (3) of Rule 80 of the CGST Rules states that, as of August 1, 2021, taxpayers whose total revenue for a fiscal year exceeds five crore rupees, must submit the annual return in FORM GSTR-9 by the thirty-first day of December after the end of the financial year, together with a self-certified reconciliation statement as required by section 44 of the CGST Act in FORM GSTR-9C.

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- When section 44 of the CGST Act and rule 80 of the CGST Rules are read together, it can be derived that, both before and after the amendment, the provisions required that registered persons who were required to submit an annual return in FORM GSTR-9 for a financial period also submit a duly certified or self-certified reconciliation statement in FORM GSTR-9C that reconciles the value of supplies declared in FORM GSTR-9 furnished for the said financial year with the audited annual financial statement. Additionally, it states that only in the event that the total turnover of the aforementioned registered person within a fiscal year surpasses the designated threshold limit must a reconciliation statement in FORM GSTR-9C be filed.
- Section 47(2) of CGST Act states that failure to file the return under section 44 of the CGST Act by the due date will result in a late charge, which will be calculated at the prescribed rate for each day that the failure goes on, up to a maximum amount. As discussed above, the annual return under section 44 of the CGST Act consists of FORM GSTR-9 in cases where a reconciliation statement in FORM GSTR-9C is not required to be furnished, and the return in FORM GSTR-9 plus a reconciliation statement in cases where a reconciliation statement in FORM GSTR-9C is required to be furnished. Therefore, the furnishing of the annual return under section 44 of the CGST Act may not be considered complete unless both the return in FORM GSTR-9 and the reconciliation statement in FORM GSTR-9C are furnished in cases where the reconciliation statement in FORM GSTR-9C is required to be furnished along with the annual return in FORM GSTR-9. The yearly return under section 44 of the CGST Act cannot be considered furnished if just the return in FORM GSTR-9 is provided and the reconciliation statement in FORM GSTR-9C is needed but not provided.
- In the context of the previously mentioned, it is made clear that the late fee under sub-section (2) of section 47 of the CGST Act is assessed for the failure to file the complete annual return under section 44 of the CGST Act, which includes both Form GSTR-9 and Form GSTR-9C (where Form GSTR-9C must also be filed). The late fee will be assessed for the time between the date on which the annual return is due and the date on which the complete annual return, which includes Forms GSTR-9 and GSTR-9C, is filed. Additionally, it should be noted that late fees for both late filing of FORM GSTR-9 and late filing of FORM GSTR-9C are not separately assessed; rather, they must be computed for the time determine between the date of the annual return’s due filing under section 44 of the CGST Act and the date of the full annual return’s filing.

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The late fee for the delayed filing of the complete annual return for any financial year up to FY 2022–2023 has been waived by notification No. 08/2025-Central Tax dated 23.01.2025. This waives the late fee that would have been due under sub-section (2) of section 47 of the CGST Act up until the date of the return’s furnishing in FORM GSTR-9 for the relevant fiscal year, provided that the reconciliation statement in FORM GSTR-9C is provided on or before March 31, 2025. As a result, in situations where the reconciliation statement in FORM GSTR-9C was supposed to be sent with the GSTR-9 return, it was not provided for any financial year before FY 2022–2023 and was provided on or before March 31st.
The late fee under section 47 will be paid until the date of FORM GSTR-9’s furnishing for the specified financial year, and no further late fee will be charged for the delayed filing of FORM GSTR-9C. Furthermore, no refunds will be given for any late fees previously paid for the financial years in question when FORM GSTR-9C was not furnished on time.