Clarification on applicability of late fee for delay in furnishing of FORM GSTR-9C

Circular No.: 246/03/2025-GST
Date of Circular: 30th January 2025
Relevant Sections and Rules:

• Section 44, CGST Act, 2017 – Annual return
• Section 47(2), CGST Act – Late fee for delay in furnishing return
• Rule 80(3), CGST Rules, 2017 – Threshold and format of GSTR-9C
• Notification No. 08/2025-Central Tax dated 23.01.2025
• Section 168(1), CGST Act – Power to issue instructions

Clarification on Late Fee Applicability for Delay in Filing FORM GSTR-9C

1. Legal Requirement for Filing GSTR-9C with GSTR-9:

• Prior to 01.08.2021:
  • Taxpayers with turnover > ₹2 crore had to get their accounts audited and file GSTR-9C (certified reconciliation statement) along with GSTR-9.
• After 01.08.2021:
  • Taxpayers with turnover > ₹5 crore are required to file a self-certified GSTR-9C along with GSTR-9.

➤ Thus, filing GSTR-9 alone does not complete the annual return where GSTR-9C is also required.

2. Applicability of Late Fee under Section 47(2):

• If GSTR-9C is required but not filed along with GSTR-9, the annual return is considered incomplete, and the late fee is applicable.
• Late fee is calculated from:
  • The due date of filing annual return (i.e., GSTR-9 and GSTR-9C)
  • Up to the actual date of filing complete return (both forms filed).

➤ Late fee is not charged separately for GSTR-9 and GSTR-9C, but for delay in filing the complete annual return.

3. Relief for Past Delays (up to FY 2022–23):

• Notification No. 08/2025-CT waives excess late fee beyond what is payable up to the date of furnishing GSTR-9, provided:
  • GSTR-9C for FYs up to 2022–23 is filed on or before 31.03.2025.

➤ No additional late fee is payable for delay in filing GSTR-9C after GSTR-9, if GSTR-9C is filed by 31.03.2025.
➤ No refund will be granted for late fees already paid for GSTR-9C delay.

Source: Circular No.: 246/03/2025-GST