CBIC Clarified on Applicability of Late Fee on Delayed Filing of GSTR-9C Up to FY 2022-23

Vide Notification No. 08/2025– Central Tax Dated 23rd January 2025, the CBIC has provided a waiver of late applicable on delayed filing of GSTR-9C up to FY 2022-23. However, CBIC received various representations seeking clarification regarding the levy of a late fee payable for delay in furnishing of reconciliation statement in FORM GSTR-9C. Many taxpayers have raised concerns regarding whether a late fee will be charged separately if GSTR-9C is not submitted along with GSTR-9 but is filed after the due date

On 30th January 2025, the Central Board of Indirect Taxes and Customs (CBIC) issued Circular No. 246/03/2025-GST to provide the following clarification on the applicability of late fees for the delayed filing of GSTR-9C:

1. Requirement to Furnish GSTR-9 and GSTR-9C

• Legal reference:
  • Section 44 of the CGST Act, 2017 – Mandates the filing of the annual return (GSTR-9) and reconciliation statement (GSTR-9C).
  • Section 47(2) of the CGST Act, 2017 – Imposes a late fee for failure to furnish the return under Section 44 within the due date.
  • Rule 80 of CGST Rules, 2017 – Specifies the threshold limit for furnishing GSTR-9 and GSTR-9C.

• Before 1st August 2021:
  • As per Section 35(5) of the CGST Act read with Rule 80(3) of CGST Rules, a registered person is required to get his accounts audited if the aggregate turnover of the registered person exceeds INR 2 Crores in a Financial year.
  • As per Section 44(2) of the CGST Act, a person who is required to get his accounts audited shall furnish the Annual Return (GSTR-9) along with a copy of audited annual accounts and a reconciliation statement (GSTR-9C).

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• From 1st August, 2021 onwards:
  • The requirement to get accounts audited for omitted.
  • Accordingly, as per Section 44(1) of the CGST Act, a registered person is required to furnish an annual return in Form GSTR-9 which may include a self-certified reconciliation statement in Form GSTR-9C.
  • As per Rule 80(3) of CGST Rules, a taxpayer with aggregate turnover exceeding INR 5 Crores is required to furnish self-certified reconciliation in Form GSTR-9C.

• Both GSTR-9 and GSTR-9C are required to be furnished on or before 31st December following the end of such a financial year.

2. When will GSTR-9 and GSTR-9C be considered as filed?

• CBIC has clarified that Section 47(2) of the CGST Act provides for a levy of a late fee for failure to furnish the return under section 44 by the due date. Late fee shall be computed at a specific rate for each day for which such failure continues subject to a maximum amount.
• Accordingly, the following shall be considered as the date of filing of the Annual Return under section 44 of the CGST Act:

3. Late fee for Filing of Annual return

• The CBIC has clarified that a late fee under section 47(2) is leviable on delay in furnishing of complete annual return, i.e., GSTR-9 and GSTR-9C. 
• It is pertinent to note that no separate late fee is leviable for delayed furnishing of GSTR-9 and GSTR-9C. However, the same shall be calculated till the date of complete filing of the annual return.
• Accordingly, a late fee shall be computed in the following manner:

• However, a practical concern may arise that the GST portal auto computes Lates fees while filing GSTR-9 only, i.e., the GST portal automatically computes late fees the date of filing of GSTR-9 only. No late fee is computed while filing GSTR-9C.
• However, If GSTR-9C is furnished after the filing of GSTR-9 after the due date then such late fee (from the date of filing GSTR-9 till the date of filing GSTR-9C) shall be imposed by the concerned field officer.

4. Government’s Relief on Late Fees

As per Notification No. 08/2025-Central Tax dated 23rd January 2025, the following relief is granted from a  late fee on filing of GSTR-9C:

• the late fee in respect of delayed filing of complete annual returns for any financial year up to FY 2022-23 has been waived, which is over the late fee payable up to the date of furnishing of return in FORM GSTR-9.
• E.g. For FY 2020-21, 

• The condition for claiming waiver is that all pending GSTR-9C up to FY 2022-23 are required to be furnished by 31st March 2025.
• However, no refund will be given for any late fees already paid for previous financial years.

5. Consequences of not filing GSTR-9C by 31st March 2025

• If the registered person fails to furnish the GSTR-9C by the due date provided under the waiver scheme, i.e., 31st March 2025, then the person is required to pay the complete amount of the late fee, i.e., till the actual date of filing of GSTR-9C.
• Businesses should ensure that they take advantage of this waiver period to avoid unnecessary financial penalties

6. Conclusion:

Timely filing of GST returns is crucial to ensure compliance and avoid penalties. Since GSTR-9C is a reconciliation statement that must be filed along with GSTR-9, any delay in its submission attracts a late fee under Section 47 of the CGST Act. Taxpayers should ensure they meet the due dates to avoid unnecessary financial burdens and maintain smooth GST compliance.