Important Keywords: Circular No. 246/03/2025 – GST, GSTR-9C late fee clarification, GSTR-9 penalty, Annual GST return delay, GST late fee rules, Finodha GST expert,
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Circular No. 246/03/2025 – GST
F. No. CBIC-20001/14/2024-GST
Government of India
Ministry of Finance
Department of Revenue
Central Board of Indirect Taxes and Customs
GST Policy Wing
*****
North Block New Delhi,
Dated the 30th January, 2025
Circular No. 246/03/2025 – GST: Clarification on applicability of late fee for delay in furnishing of FORM GSTR-9C
To,
All the Principal Chief Commissioners/ Chief Commissioners
All the Principal Directors General/ Directors General
Madam/Sir,
Subject: Clarification on applicability of late fee for delay in furnishing of FORM GSTR-9C- reg.
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 requested to clarify whether late fee under section 47 of Central Goods and Services Tax Act, 2017 (hereinafter referred to as the “CGST Act”) will be leviable where reconciliation statement in FORM GSTR-9C is not furnished by the registered person alongwith the annual return in FORM GSTR-9 but is filed subsequently beyond the due date of furnishing of annual return.
2. In order to ensure uniformity in the implementation of the provisions of law across the
field formations, the Board, in exercise of its powers conferred by sub-section (1) of section
168 of the CGST Act, hereby clarifies the issues as below.
3 Prior to 01.08.2021, sub-section (2) of section 44 of CGST Act provided that a registered person who is required to get his accounts audited in accordance with the provisions of sub-section (5) of section 35 of the CGST Act shall furnish the annual return under sub-section (1) of the said section along with a copy of the audited annual accounts and a reconciliation statement.
From 01.08.2021 onwards, with the omission of the requirement of getting accounts audited in accordance with the provisions of sub-section (5) of section 35 of the CGST Act, sub-section (1) of section 44 of CGST Act provides for furnishing of annual return which may include a self-certified reconciliation statement, reconciling 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 such time and in such form and in such manner as may be prescribed.
Further, before 01.08.2021, sub-rule (3) of rule 80 of Central Goods and Services Tax Rules, 2017 (hereinafter referred to as the “CGST Rules”) provided that accounts shall be audited as per sub-section (5) of section 35 of the CGST Act in case the aggregate turnover of a registered person exceeded two crore rupees in a financial year and such taxpayer shall furnish a copy of audited annual accounts and a reconciliation statement, duly certified, in FORM GSTR-9C.
From 01.08.2021 onwards, sub-rule (3) of rule 80 of CGST Rules provides that taxpayer with aggregate turnover during a financial year exceeding five crore rupees, shall furnish a self certified reconciliation statement as specified under section 44 of the CGST Act in FORM GSTR-9C along with the annual return in FORM GSTR-9 on or before the thirty-first day of December following the end of such financial year.
3.1 Therefore, on a combined reading of section 44 of CGST Act with rule 80 of the CGST Rules, it can be concluded that both pre and post amendment, the provisions mandated that registered persons required to furnish an annual return in FORM GSTR-9 for a financial year shall also furnish along with it, a duly certified or self-certified reconciliation statement in FORM GSTR-9C, which reconciles the value of supplies declared in FORM GSTR-9 furnished for the said financial year with the audited annual financial statement.
It is also mentioned that a reconciliation statement in FORM GSTR-9C is required to be filed only if the aggregate turnover of the said registered person during a financial year exceeds the specified threshold limit.
3.2 Sub-section (2) of section 47 of the CGST Act provides for a levy of a late fee for failure to furnish the return under section 44 of the CGST Act by its due date, which is to be computed at the specified rate, for each day for which such failure continues, subject to a maximum amount.
As per the discussions above, in cases where reconciliation statement in FORM GSTR-9C is not required to be furnished, annual return under section 44 of CGST Act consists only of FORM GSTR-9 and in cases where a reconciliation statement in FORM GSTR-9C is required to be furnished, the annual return under section 44 of CGST Act consists of the return in FORM GSTR-9 along with a reconciliation statement in FORM GSTR-9C.
Therefore, 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 furnishing of annual return under section 44 of the CGST Act, may not be said to be complete, unless both return in FORM GSTR-9 and reconciliation statement in FORM GSTR-9C are furnished. If only return in FORM GSTR-9 is furnished and reconciliation statement in FORM GSTR-9C is required but not furnished, annual return under section 44 of CGST Act cannot be said to have been furnished.
3.3 In view of the above, it is clarified that late fee under sub-section (2) of section 47 of the CGST Act, is leviable for the delay in furnishing of complete annual return under section 44 of the CGST Act, i.e. both FORM GSTR-9 and FORM GSTR-9C (where FORM GSTR 9C is also required to be furnished) and the late fee shall be payable for the period from the due date of furnishing of the said annual return upto the date of furnishing of the complete annual return i.e. FORM GSTR-9 and FORM GSTR-9C.
It is also to be noted that late fee is not separately leviable for delayed furnishing of FORM GSTR-9 and delayed furnishing of FORM GSTR-9C, but has to be calculated for the period from the due date of furnishing of annual return under section 44 of the CGST Act till the date of furnishing of complete annual return i.e.:
i. in cases where FORM GSTR-9C is not required to be furnished, the date of furnishing of FORM GSTR-9;
ii. in cases where FORM GSTR-9C is required to be furnished along with FORM GSTR-9,
a. the date of furnishing of FORM GSTR-9, if FORM GSTR-9C is furnished alongwith FORM GSTR-9; or
b. the date of furnishing of FORM GSTR-9C, if FORM GSTR-9C is furnished subsequent to furnishing of FORM GSTR-9.
It is further mentioned that vide notification No. 08/2025-Central Tax dated 23.01.2025, the late fee in respect of delayed filing of complete annual return for any financial year upto FY 2022-23 has been waived, which is in excess of the late fee payable under sub-section (2) of section 47 of CGST Act upto the date of furnishing of return in FORM GSTR-9 for the said financial year, if the reconciliation statement in FORM GSTR 9C is furnished on or before 31st March 2025.
Accordingly, in cases where reconciliation statement in FORM GSTR-9C was required to be furnished along with the return in FORM GSTR-9, but was not furnished so for any financial years upto FY 2022-23, and has been furnished subsequently on or before 31st March, 2025, then no additional late fee shall be payable for delayed furnishing of FORM GSTR-9C which is in excess of the late fee payable under section 47 upto the date of furnishing FORM GSTR-9 for the said financial year. Further, no refund shall be admissible in respect of any amount of late fee already paid in respect of delayed furnishing of FORM GSTR-9C for the said financial years.
5. It is requested that suitable trade notices may be issued to publicize the contents of this Circular.
6. Difficulty, if any, in the implementation of this Circular may be brought to the notice of the Board.
Yours faithfully,
Gaurav Singh
Commissioner (GST)
Frequently Asked Questions (FAQs): Circular No. 246/03/2025 – GST
Q1: What does Circular No. 246/03/2025-GST clarify?
Answer:
It clarifies that no separate late fee is prescribed under the CGST Act for delay in furnishing GSTR-9C (Reconciliation Statement). The late fee is applicable only for delay in GSTR-9 (Annual Return) under Section 47(2) of the Act.
🧾 For professional return filing: https://finodha.in/gst-return-filing/
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Q2: Is late filing of GSTR-9C penalized under GST?
Answer:
No separate late fee is imposed on GSTR-9C filing delay. As per the clarification, late fee is applicable only for GSTR-9. GSTR-9C has to be filed along with GSTR-9. Hence, timely GSTR-9 filing ensures no penalty.
💼 Need clarity on return timelines? Visit: https://finodha.in/gst-compliance/
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Q3: What does Section 47(2) of the CGST Act state?
Answer:
Section 47(2) specifies late fee for failing to furnish the annual return (GSTR-9). There is no explicit provision for late fee on GSTR-9C. Therefore, the delay in GSTR-9C does not attract an independent fee.
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Q4: Can I file GSTR-9C after GSTR-9 without incurring a separate penalty?
Answer:
Yes ✅. As per this circular, GSTR-9C accompanies GSTR-9, and the late fee applies to the latter. No separate penalty exists for delayed GSTR-9C alone.
🔍 Avoid penalty! Get expert help: https://finodha.in/gst-return-filing/
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Q5: What if I submitted GSTR-9C late in the past—do I pay a late fee?
Answer:
If GSTR-9 was filed late, late fee applied under Section 47(2). GSTR-9C filing delay alone, without GSTR-9 delay, should not attract any late fee, as per this new clarification.
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Q6: What is the purpose of GSTR-9C?
Answer:
GSTR-9C is a reconciliation statement between the taxpayer’s audited annual financial statements and the GSTR-9 return. It’s mandatory for taxpayers exceeding prescribed turnover thresholds.
📊 Need help preparing GSTR-9C with CA attestation? Consult Finodha: https://finodha.in/online-gst-registration/
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Q7: Who must file GSTR-9C under GST?
Answer:
All registered persons with aggregate turnover exceeding ₹5 crore (as per FY 2022–23 guidelines) are required to submit GSTR-9C, certified by a CA/CMA.
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Q8: Is GSTR-9C filing mandatory if GSTR-9 is filed?
Answer:
Only if your turnover exceeds the prescribed limit. If below ₹5 crore (as updated per recent notifications), GSTR-9C is not required even if GSTR-9 is filed.
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✅ Final Summary:
Circular No. 246/03/2025 – GST clearly resolves doubts regarding the levy of late fee on GSTR-9C. It reaffirms that late fee under Section 47(2) is applicable solely to GSTR-9 and not GSTR-9C. This ensures fairness and reduces unnecessary financial burden on taxpayers.
💡 Stay ahead with accurate GST filing support. Contact Finodha GST Experts:
🔹 GST Advisory: https://finodha.in/gst-compliance/
🔹 ROC & Annual Compliance: https://finodha.in/roc-compliance-for-private-limited-company/
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Download PDF: Circular No. 246/03/2025 – GST
More Information: https://taxinformation.cbic.gov.in/
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