Regarding non filing of GSTR-9C (but GSTR-9 filed) Sec-47 Penalty for non filing of return u/s 44

Step 1:Section 47 of the GST Act states that any registered person who fails to furnish a return under section 44 shall pay a late fee of Rs.100 for every day during which such failure continues, subject to amaximum of Rs.5,000/-

Step 2: Analyze Circular

Step 3:Determine the Penalty for Non-Filing of GSTR-9C: 

Thanks for the immediate reply. 

GSTR-9C is treated as part of the annual return requirement under Section 44. Not filing GSTR-9C when required exposes you to a late fee under Section 47.

HERE IS HOW THE LATE FEE WORKS:
- Late fee is Rs 200 per day (Rs 100 CGST plus Rs 100 SGST) for non-filing of annual return
- Maximum cap: Rs 0.25% of turnover in the state (for CGST) plus Rs 0.25% of turnover (for SGST)
- GSTR-9C non-filing is treated as incomplete compliance for the year, even if GSTR-9 was filed on time

BUT NOTE: GST Council has repeatedly waived late fees through amnesties. Check whether an active amnesty or waiver notification covers your period. For FY 2023-24 and earlier, several notifications have reduced or waived late fees for deferred filers.

PRACTICAL STEPS IF GSTR-9C IS STILL PENDING:
1. File immediately. The late fee stops accruing from the date of filing.
2. Check the GST portal for any active late fee waiver notification for your turnover slab and financial year.
3. Compute the late fee using the total number of days from the due date (December 31) to the filing date.

For the full late fee and penalty structure across GST returns, see this [guide to GST, TDS, and ROC filing penalties](https://taxgarden.in/blog/true-cost-late-gst-tds-roc-filing-penalties-india-2026).

The legal position after the 2025 clarification:

• From FY 2020-21, GSTR-9C is a self-certified reconciliation statement furnished along with GSTR-9 under Sec 44 read with Rule 80(3). CBIC Circular 246/03/2025-GST (30 January 2025) clarifies that the annual return is complete only when 9C is furnished, where required. So late fee under Sec 47(2) runs until 9C is filed.

• Relief: Notf 08/2025-CT waived the late fee beyond what was already paid for FY 2017-18 to 2022-23, where GSTR-9C was filed by 31 March 2025.

• Your argument that 9C is not a "return" under Sec 47 has support in the text. But after the amended Rule 80(3), courts have yet to decide it finally. Litigation is uncertain.

• Practical: file 9C now if turnover exceeds Rs 5 crore. Late fee (Notf 07/2023-CT) is Rs 100 per day (combined) capped at 0.04% of State turnover for AATO of Rs 5–20 crore, and Rs 200 per day capped at 0.5% above Rs 20 crore.