General Penalty for delayed filing of GSTR-9C for FY 2022-23

[Shyam Naik]

There was a delay of filing Annual Return by 30 days and the applicable late fee was remitted. The GSTR-9C was filed after 2 days of filing the GSTR-9. A Audit Objection has been served proposing General Penalty of Rs. 25,000/- each under CGST and SGST.

How the imposition of penalty can be contested. Pls guide.

[Sadanand Bulbule]

The proposed general penalty under Section 125 is legally unsustainable because the 30-day delay in filing Form GSTR-9 and the subsequent 2-day gap for Form GSTR-9C represent a minor, fully rectified procedural omission with zero revenue loss, which has already been statutorily regularized through the payment of specific late fees under Section 47(2), thereby precluding any parallel residual penalization under settled judicial precedents.

 

[Raam Srinivasan Swaminathan Kalpathi]

Dear Querist

There is a legal precedent which embars levy of Sec.125 general penalty for cases involving late fees remittance u/s.47. Recently the Madras High Court in the case of Kandan Hardware Mart ruled emphatically that late fees is penal and there can be no additional penalty compounding this. The HC ruled that tax authorities cannot simultaneously impose general penalty u/s.125 alongside late fees u/s.47. Another case law reference will be Kalanther Madeena Textiles v. The Deputy Commissioner (CT) reported as 2026 (3) TMI 722 rep by its prop. Kalanther Naina Mohamed (Mad HC). Request you to go through the above case laws and contest the levy. You may also refer to an Article published at TMI by Sri.Chitresh Gupta on 13-Apr-26. Thanks

[Kashish Gupta]

The imposition of a general penalty under Section 125 of the CGST Act is not sustainable in the present facts and circumstances for the reasons which are four-fold.

Firstly, it can be pleaded that the delay in filing FORM GSTR-9C was minute, being only 2 days, after the filing of FORM GSTR-9. Reliance can be placed on Section 126 of CGST Act which provides for "General disciplines related to penalty".

Secondly, present case pertains to FY 2022-23 for which a specific relaxation is notified vide Notification No. 08/2025-Central Tax dated 23.01.2025. Said notification provides that in cases where FORM GSTR-9C, though required to be furnished along with FORM GSTR-9, was furnished subsequently but on or before 31st March 2025 for any financial year upto FY 2022-23, no additional late fee shall be payable beyond the late fee payable upto the date of furnishing FORM GSTR-9. Therefore, if FORM GSTR-9C is filed on or before 31.03.2025 (which should have been as you have mentioned that FORM GSTR-9 is filed with a delay of 30 days i.e., on 30.01.2024 (31.12.2023 being the due date for filing of GSTR-9 for FY 2022-23) and FORM GSTR-9C is filed with delay of 2 days i.e., on 02.02.2024), benefit of notification shall enure to you.

Thirdly, CBIC vide its Circular No. 246/03/2025-GST dated 30.01.2025 has clarified that FORM GSTR-9 and FORM GSTR-9C together constitute a single integrated Annual Return under Section 44 of CGST Act, and that imposition of late fee under Section 47(2) covers the entire period of delay in furnishing such complete return, i.e., both FORM GSTR-9 and FORM GSTR-9C. Since Section 125 is a residuary provision, its invocation is impermissible where Section 47(2) specifically governs the consequence of delay in furnishing the Annual Return.

Fourthly, Hon'ble Madras High Court in the matter of Kalanther Madeena Textiles v. The Deputy Commissioner (CT) reported as 2026 (3) TMI 722 categorically held that once late fee under Section 47(2) of the respective GST enactments has been levied (irrespective of concessions given under a Notification), there remains no scope for the imposition of a separate general penalty under Section 125 for the very same default.

Accordingly, a suitable reply to the audit objection on the aforesaid grounds, along with the necessary relied upon documents and above mentioned statutory provisions, Notification and Circular should suffice for waiver of the proposed penalty.

[Ryan Vaz]

The proposed penalty can be contested on the ground that the GST law already prescribes a specific statutory consequence - namely late fee under Section 47 - for delayed filing, and the same has already been discharged.

Further, delayed filing of GSTR-9C by 2 days after filing GSTR-9 is a procedural and technical lapse without revenue implication, fraud, suppression, or tax evasion. Therefore, invocation of Section 125 general penalty is legally excessive and contrary to Section 126 principles of proportionality.

[Suresh Yadav]

Please go through Circular No. 246/03/2025-GST dated 30.01.2025.

[KALLESHAMURTHY MURTHY K.N.]

Sir,

Late fee under Sec. 47(2) is leviable for the delayed period for both Form 9 and 9C, till the date of filing of both returns, wherever they are required to be filed, but cannot be calculated separately for both returns. If any one of the returns filed belatedly, the period is to be reckoned for the returns last filed, either Form 9 or Form-9C, from the due date of the annual return to be filed u/s 44 of the CGST Act. However, returns already filed before 31-03 2025, no additional or excess fee is payable for the delayed period as per Notification No. 08/2025-Central Tax dated 23.01.2025 for the periods up to 2022-23.

In the instance case, the GSTR-9C was filed 2 days after the GSTR-9 was filed. So the delayed period is to be reckoned up to the date of GSTR-9C filed, and the late fee is payable for this period (if filed after 31-03-2025), but not payable separately for individual returns.

Levy of Rs. 25000-00 +250000-00 is now not in vogue as per the clarification in Circular No. 246/03/2025-GST dated 30-01-2025.

[Shilpi Jain]

Where there is already a late fee in the law for late filing of 9 & 9C again a general penalty cannot be levied. This is the relevant decision Tvl. Jainsons Castors & Industrial Products Versus The Assistant Commissioner (ST) (2025 (2) TMI 1000 - MADRAS HIGH COURT)

 

[Shilpi Jain]

This GSTR-9 & 9C delay is for which year? Since the late fee provisions have recently been amended.

Suggested that you have a look at Circular No. 246/03/2025-GST dated 30.01.2025 in this regard.

[KALLESHAMURTHY MURTHY K.N.]

Sir,

Madras HC held that the benefit of the notifications should extend to taxpayers who filed returns before 01.04.2023 in the case of SVR Developers Vs Assistant Commissioner (FAC) - 2026 (6) TMI 99 - MADRAS HIGH COURT and that the General Penalty under GST is invalid when a "Late Fee" is specifically prescribed against the order passed on 22-04-2024 pertaining to the period 2018-19.

AI Summary

GST late fee for delayed GSTR-9C filing may exclude separate general penalty under the CGST Act. Late filing of GSTR-9 and subsequent filing of GSTR-9C raised the issue whether a separate general penalty under section 125 of the CGST Act can be imposed after late fee has already been paid for the delay. The discussion states that where late fee is specifically prescribed under section 47 for delayed annual return filing, the residuary general penalty is not sustainable for the same procedural default. It also refers to a relaxation for FY 2022-23 and to a CBIC circular treating GSTR-9 and GSTR-9C as a single integrated annual return for late fee purposes.