Madras High Court
WP/37291/2026 of M/S.Vellore Agro Marketing, Represented by its Par Vs The Commercial Tax Officer on 28 September 2026
WP No. 37291 of 2026
IN THE HIGH COURT OF JUDICATURE AT MADRAS
DATED: 28-09-2026
CORAM
THE HON'BLE MR JUSTICE SENTHILKUMAR RAMAMOORTHY
WP No. 37291 of 2026
and W.M.P.No.41882 of 2026
CNR: {HCMA011946802026}
M/S.Vellore Agro Marketing,
Represented by its Partner MR.Venkatesan Ashok, No. 42C ,Mambalapattu Road , Villupuram - 605 602.
..Petitioner(s)
Vs
The Commercial Tax Officer,
Villupuram - I Assessment Circle,
Villupuram.
..Respondent(s)
PRAYER: Writ Petition filed under Article 226 of The Constitution of India praying for the issuance of a Writ of Certiorarified Mandamus, To call for the impugned Deficiency Memo issued by the respondent in Form GST RFD-03
dated 07.04.2025 bearing Deficiency Memo Number ZD330425060618Dand quash the impugned proceedings as passed contrary to the provisions of the CGST/TNGST Act, 2017, and against the principles of natural justice and further direct the respondent to refund the excess CGST of Rs.1,80,660 and excess SGST of Rs.1,80,660/- to the petitioner.
For Petitioner(s):
Mr.Samuel Rupesh Rajkumar
WP No. 37291 of 2026
For Respondent(s):
Mr.R.Sethu Prabakaran,
Government Advocate (Tax)
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ORDER
Deficiency memo dated 07.04.2025 in response to refund application dated 29.02.2024 is assailed in this writ petition.
2. Learned counsel for the petitioner submits that the deficiency memo was issued beyond the 15 day time limit fixed in sub-rules (2) and (3) of Rule 90 of applicable GST Rules.
3. Mr.R.Sethu Prabakaran, learned Government Advocate (Tax), accepts notice for the respondent. He points out that the petitioner is within the time limit specified in Section 54(1) of applicable GST statutes read with sub-rule (3) of Rule 90.
4. As per the proviso to sub-rule (3) of Rule 90, the period running from the date of filing of the refund application till the date of communication of the deficiencies in Form GST RFD-03 shall be excluded while computing the period of two years in sub-section (1) of Section 54. Both parties submit that
WP No. 37291 of 2026
after such exclusion, the petitioner would still be in a position to file a refund application.
5. Taking note of this fact, this writ petition is disposed of by leaving it open to the petitioner to file a fresh refund application in accordance with sub- section (1) of Section 54 read with the proviso to sub-rule (3) of Rule 90 after rectifying the deficiencies, if any, pointed out in the impugned deficiency memo. If the petitioner encounters any difficulty in uploading the refund application on the portal, a grievance may be raised in that regard. Any such grievance shall be redressed within a reasonable period. Consequently, the connected writ miscellaneous petition is closed. There shall be no order as to costs. 28-09-2026 Index: Yes/No Speaking/Non-speaking order Neutral Citation: Yes/No RNA To The Commercial Tax Officer, Villupuram - I Assessment Circle, villupuram.
WP No. 37291 of 2026
SENTHILKUMAR RAMAMOORTHY, J. RNA WP No. 37291 of 2026 and W.M.P.No.41882 of 2026 28-09-2026