TaxTMI 
TaxTMI 
2026 (1) TMI 102
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....me and thus must be sanctioned in full; (ii) Quashing the impugned order in Form GST RFD-06 dated 18.04.2023 passed by the 1st Respondent under Rule 92 of the CGST Rules, 2017, read with Section 54 of the CGST Act, 2017 (Annexure M), insofar as it rejects the refund of Rs.14,24,564/- that was rightly claimed by the Petitioner; (iii) Quashing the impugned order dated 24.07.2023 passed by Respondent No.1 bearing F.No.GEXCOM/TECH/MISC/2347/2023-CGST-RANGEASD5-DIV-SD5-COMMRT-BENGALURU(S) and DIN No.20230757YV0000022876/2592 (Annexure R); (iv) Condoning the delay of 3 days in filing the refund claim dated 09.02.2023 bearing ARN AA290223029829X (Annexure G-2); In either case, (v) Directing Respondent N....
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....ction of the refund claim and the said rectification request was also rejected by the respondent No.1 vide the impugned order dated 24.07.2023. Aggrieved by the impugned order dated 18.04.2023 at Annexure - M, the petitioner is before this Court by way of the present petition . 5. A perusal of the material on record including the impugned order will indicate that the sole reason assigned by respondent No.1 in rejecting the refund claim of the petitioner is by coming to the conclusion that the same was barred by limitation. 6. Under identical circumstances, this Court in the case of M/s. Merck Life Science Private Limited v. The Union of India and others in W.P.No.27259/2024 and connected matters dated 07.11.2025, has held as under: ....
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.... A registered person who has paid central tax and State tax or Union territory tax, as the case may be, on a transaction considered by him to be an intra-State supply, but which is subsequently held to be an inter-State supply, shall not be required to pay any interest on the amount of integrated tax payable." Rule 89(1A) of the CGST Rules: 89(1A). Any person, claiming refund under section 77 of the Act of any tax paid by him in respect of a transaction considered by him to be an intra-State supply, which is subsequently held to be an inter-State supply, may, before the expiry of a period of two years from the date of payment of the tax on the inter-State supply, file an application electronically in FORM GST RFD-01 throug....
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....54 of the CGST Act, which provide a period of 2 years is directory and not mandatory. 18. It is also pertinent to note that in the Statement of Objections filed by the respondents in all these petitions, the payment in excess made by the petitioner to the Central Authorities, though not contested, have not been disputed by the Central Authorities as can be seen from paragraph No.11 of all respective petitions, one of which (W.P.No.27259/2024) reads as under: 11. It is further submitted that the respondent has not contested that the petitioner has paid Rs.52,63,596/- under IGST Head in excess whereas the same was later discharged under the correct head of CGST and SGST during March 2018. Respondent agrees that the tax was d....
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.... GST Authorities towards IGST prior to making similar payment to the State GST Authorities. 20. As held by the High Court of Madras and the High Court of Andhra Pradesh in the aforesaid judgments, Section 54 of the CGST Act and Rule 89(1A) of the CGST Rules, 2017 have been held to be directory and not mandatory. It is also significant to note that having regard to Article 265 of the Constitution of India, the respondent -.Central GST authorities were not entitled to collect IGST form the petitioner, who was not liable to pay the same and consequently, upon the petitioner paying the same amount to the State GST authorities subsequently, the respondent -.Centre was not entitled to retain the IGST and consequently, by applying the pri....
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.... 24. In the result, I pass the following: ORDER (i) These petitions are hereby allowed. (ii) The impugned orders bearing No.31/2024-25 dated 27.05.2024; No.29/2024-25 dated 25.05.2024; No.30/2024-25 dated 27.05.2024; No.27/2024-25 dated 25.05.2024; No.28/2024- 25 dated 25.05.2024 passed by respondent No.3 are hereby set aside. (iii) It is held that the refund application/claim of the petitioner is not barred by limitation. (iv) The matters are remitted back to respondent No.3 for passing appropriate orders on the refund application filed by the petitioner, bearing in mind the observations made in the body of this order and in accordance with law, within a period of three (3) months from the date of re....