The CBIC issued Clarification vide Circular No. 46/03/2025-GST dated 30.01.2025, addressing how late fees under Section 47(2) of the CGST Act are applied for delays in filing the complete annual return (i.e., both FORM GSTR-9 and FORM GSTR-9C, where applicable).

The Circular provides clarifications as under:

A. Applicability of Late Fees:

• Late Fee is Computed for the Complete Annual Return i.e. FORM GSTR-9 and FORM GSTR-9C (if required based on turnover).
• Late fees are not levied separately for delays in filing GSTR-9 and GSTR-9C. Instead, the fee is calculated based on the delay in filing the complete return.

B. Scenarios for Late Fee Calculation:

• When FORM GSTR-9C is NOT Required: Filing is considered complete when FORM GSTR-9 is filed. Late fee is calculated from the due date of FORM GSTR-9 to the actual filing date of FORM GSTR-9.
• When FORM GSTR-9C is Required: Filing is considered complete only when both FORM GSTR-9 and FORM GSTR-9C are filed. Late fee is calculated from the due date of the annual return to the:
  • Date of filing FORM GSTR-9, if GSTR-9C is filed simultaneously.
  • Date of filing FORM GSTR-9C, if filed after FORM GSTR-9.

C. Waiver of Late Fees for Past Years (vide Notification No. 08/2025-Central Tax dated 23.01.2025):

• Late fees exceeding the specified rate under Section 47(2) are waived for financial years up to FY 2022-23, provided FORM GSTR-9C is furnished on or before March 31, 2025.
• For taxpayers who file FORM GSTR-9C by this date, no additional late fees will apply.
• Refund Provisions: No refunds will be provided for late fees already paid.

The Complete Circular can be accessed at https://taxo.online/wp-content/uploads/2025/01/cir-cgst-246-03-2025.pdf