Can Penalty be Levied on Delayed Annual GST Return
                     Can Penalty be Levied on Delayed Annual GST Return?
Industry has recently filed 8th annual return on or before 31st December, 2025. This sphere of GST law has seen 
many ups and downs in terms of extension of due dates, changes in late fees, amnesty to file pending 
returns and recently computation of late fees where annual return filed but not reconciliation statement. It 
is often advocated in the legal circles that two penalties can not be imposed for the same offence. Here 
under this segment of compliances, two documents are filed, annual return in form GSTR-9 and 
reconciliation statement in form GSTR-9C. It is usually perceived that these two forms are different but 
recently department has clarified this by way of circular that annual return is the primary form and 
reconciliation statement is the attachment to annual return wherever applicable. Two provisions of the law 
are relevant here, section 47 and section 125 of the CGST Act. In this article, author has dwelled on this 
issue only basis two important judgements passed by the honorable Madras High Court.
Question which is addressed by the court is, “Where assessee failed to file annual return and was levied late fee 
under section 47 of CGST and SGST, whether imposition of additional general penalty under section 125 was 
permissible since a specific penalty was already provided for same contravention, and so as general penalty 
was to be quashed and only specific late fee was sustainable? Facts of the Case [2026] 182 taxmann.com 
321 (Madras) HIGH COURT OF MADRAS Tvl R P G Traders v. State Tax Officer Petitioner failed to file annual 
returns – Department levied late fee under section 47 and general penalty under section 125 – Petitioner 
contended that as per section 47, only late fee could be levied and further section 125 would apply where 
no penalty is levied under section 47 – Petitioner submitted that without proper enquiry and verification of 
records, respondent passed impugned order. The learned counsel appearing for the petitioner would 
submit that since the petitioner failed to file its annual returns, the first respondent passed the impugned 
order by levying the penalty fee of Rs.75,025/- CGST and Rs.75,025 of SGST, totalling to Rs.1,50,050/-along 
with general penalty of Rs.50,000/-. He further submits that as per Section 47 of the TNGST Act, 2017, only 
late fee can be levied. Further, the provision under Section 125 of the Act will apply only in the case where 
no penalty is levied under Section 47 of the Act. He further submits that without proper enquiry and 
verification of records as contemplated under Section 73 of the GST Act, the 1st respondent has passed the 
impugned order. Therefore, the impugned order is liable to be quashed.
The learned Additional Government Pleader appearing for the first respondent would submit that since the petitioner 
failed to file its annual returns, the impugned order has been passed levying the late fee along with general penalty. 
Therefore, he prays for dismissal of the Writ Petition. Discussion and Judgement On a perusal of the records, it is 
seen that since the petitioner failed to file its annual returns, as per Section 47 of the Act, the first respondent has 
levied the late fee of Rs.75,025/- CGST and Rs. 75,025/- of SGST, totalling to Rs.1,50,050/-. Further, under Section 125 
of the Act, the first respondent has levied the general penalty of Rs.25,000/- CGST and Rs.25,000/- of SGST, totalling 
to Rs.50,000/-.
In this regard, the petitioner has also produced the order passed by the Principal Bench of this Court in W.P.No.36614 
of 2024, dated 04.02.2025/Tvl. Jainsons Castors & Industrial Products v. Assistant Commissioner (ST) [2025] 172 
taxmann.com 358 (Madras)/[2025] 98 GSTL 110 (Madras). Relevant para from the case is reproduced here for ready 
reference-: 7. In the event of non-filing of the return, the respondent can call upon the petitioner to pay the late fee 
in terms of Section 47 of the Act, which is independent provision deals with any default or belated filing of return. 
Therefore, this Court does not find any fault in the show cause notice issued by respondent under Section 47 r/w 73 
of the Act. The respondent is entitle to initiate proceedings as per applicable provision for non-filing of return. 
However, in the present case, the respondent has imposed the late fee under Section 47 of the Act and also penalty 
under Section 125 of the Act. At this juncture, it is relevant to extract Section 125 of the Act, which reads as follows
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“125. Any person, who contravenes any of the provisions of this Act or any rules made thereunder for which no 
penalty is separately provided for in this Act, shall be liable to a penalty which may extend to twenty five 
thousand rupees.” A reading of the above would show that in the event no penalty is separately provided 
in this act, general penalty would apply. In the present case, penalty was imposed in the form of late fee in 
terms of Section 47 of the Act. Therefore, general penalty of Rs.50,000/- towards CGST and SGST is not 
correct and the same is set aside. As far as late fee is concerned, the same is confirmed.
This Court is of the view that the provision under Section 125 of the Act, apply only in the case where no 
penalty is levied under Section 47 of the Act. However, in this case, already late fee has been levied under 
Section 47 of the Act. Therefore, the question of levying general penalty under Section 125 of the Act will 
not apply. Therefore, the same is liable to be quashed. Accordingly, the levying of general penalty of 
Rs.50,000/- is hereby set aside. Conclusion According to both judgements passed by honorable court, it is 
firmly decided that penalty under section 125 shall only be levied under those situations where no other 
penalty is prescribed for a particular offence. Here under section 47 of the act, late fees is prescribed for 
delayed filing of annual return, now if, filing is delayed and late fees charged then section 125 can not be 
invoked and general penalty can be charged. Ratio laid down by these two judgements wont only apply to 
annual return matters but other offences also in which late fees or other fine is prescribed and charged.
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