Bombay High Court Allows Refund of Accumulated Input Tax Credit Under Inverted Duty Structure in GST — Rejection by Authorities Set Aside. Held that refund of unutilized ITC is admissible under Section 54(3)(ii) of the CGST Act, 2017 even when output supply is partially exempt, and that the formula under Rule 89(5) of the CGST Rules, 2017 must be applied correctly.

High Court: Bombay High Court Bench: BOMBAY In Favour of Accused
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Case Note & Summary

The petitioner, CHEC-TPL Line 4 Joint Venture, a joint venture between TATA Projects Limited and another entity, was engaged in the construction of a tunnel for the Mumbai Metro Rail Corporation Limited. The petitioner was registered under the GST laws and had accumulated a large amount of input tax credit (ITC) due to the inverted duty structure, where the tax rate on inputs (18%) was higher than the tax rate on output supplies (12% for construction services). The petitioner filed refund claims for the unutilized ITC for the periods July 2017 to March 2018 and April 2018 to June 2018 under Section 54(3)(ii) of the Central Goods and Services Tax Act, 2017 (CGST Act). The Original Authority (Assistant Commissioner) rejected the refund claims on the ground that the output supply was partially exempt, and therefore the refund was not admissible. The petitioner appealed to the Appellate Authority (Joint Commissioner), who upheld the rejection. Aggrieved, the petitioner filed a writ petition under Article 226 of the Constitution of India before the Bombay High Court. The main legal issues were whether the refund of accumulated ITC under inverted duty structure is admissible when the output supply is partially exempt, and whether the formula under Rule 89(5) of the CGST Rules, 2017 was correctly applied. The petitioner argued that the authorities had misinterpreted the provisions and that the refund was clearly admissible. The respondents defended the rejection, contending that the output supply being partially exempt disentitled the petitioner to refund. The High Court analyzed Section 54(3)(ii) and Rule 89(5) and held that the refund is admissible even if the output supply is partially exempt, as long as the conditions are met. The court found that the authorities had erred in excluding certain supplies from the 'Adjusted Total Turnover' and in computing 'Net ITC'. The court quashed the impugned orders and remanded the matter to the Original Authority for fresh consideration in accordance with the law, directing that the refund be computed correctly. The petition was allowed.

Headnote

A) GST - Refund of Accumulated ITC - Inverted Duty Structure - Section 54(3)(ii) CGST Act, 2017 - Rule 89(5) CGST Rules, 2017 - The petitioner, a joint venture engaged in construction, sought refund of unutilized input tax credit accumulated due to higher rate of tax on inputs than on output supplies. The authorities rejected the claim on the ground that the output supply was partially exempt. The High Court held that the refund is admissible under Section 54(3)(ii) even if the output supply is partially exempt, and that the formula under Rule 89(5) must be applied correctly to compute the refundable amount. The impugned orders were quashed and the matter remanded for fresh consideration. (Paras 1-17)

B) GST - Refund Formula - Net ITC - Adjusted Total Turnover - Rule 89(5) CGST Rules, 2017 - The court clarified that 'Net ITC' means input tax credit availed on inputs during the relevant period, and 'Adjusted Total Turnover' includes the value of exempt supplies. The authorities had erred in excluding certain supplies from the turnover. The court directed the authorities to recompute the refund in accordance with the correct interpretation of the rule. (Paras 10-15)

C) Constitutional Law - Writ Jurisdiction - Article 226 of Constitution of India - The court exercised its writ jurisdiction to quash the orders-in-original and order-in-appeal as they suffered from errors of law and misinterpretation of statutory provisions. The court held that the rejection of refund was arbitrary and not sustainable. (Paras 2, 16-17)

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Issue of Consideration

Whether the rejection of refund claims for accumulated input tax credit due to inverted tax structure by the Original Authority and Appellate Authority was valid under Section 54(3)(ii) of the CGST Act, 2017 and Rule 89(5) of the CGST Rules, 2017.

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Final Decision

The High Court allowed the writ petition, quashed the Order-in-Appeal dated 31.10.2023 and the Order-in-Original, and remanded the matter to the Original Authority for fresh consideration in accordance with the law. The court directed that the refund be computed correctly applying the proper interpretation of Section 54(3)(ii) and Rule 89(5).

Law Points

  • Refund of accumulated input tax credit under inverted duty structure
  • Section 54(3)(ii) of CGST Act
  • 2017
  • Rule 89(5) of CGST Rules
  • Net input tax credit
  • Adjusted total turnover
  • Constitutional validity of refund provisions
  • Article 226 of Constitution of India
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Case Details

2026 LawText (BOM) (04) 60

Writ Petition No.2583 of 2025

2026-04-23

G. S. Kulkarni, Aarti Sathe

Mr. Prasad Paranjape with Mr. Kevin Gogri, Mrs. Dhruvi Shah i/by Lumiere Law Partners for Petitioner; Mrs. Shehnaz V. Bharucha and Ms. Niyati Mankad with Ms. Priyanka Singh for Respondents

CHEC-TPL Line 4 Joint Venture

Union of India through Ministry of Finance, Department of Revenue; The Joint Commissioner, Central Tax (Raigad Appeals); The Assistant Commissioner of CGT & C.Ex.; The Commissioner of CGST & C.Ex.

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Nature of Litigation

Writ petition under Article 226 of the Constitution of India challenging the rejection of refund claims for accumulated input tax credit due to inverted duty structure under GST.

Remedy Sought

The petitioner sought a writ of certiorari to quash the Order-in-Appeal dated 31.10.2023 and the Order-in-Original, and to direct the respondents to grant the refund.

Filing Reason

The petitioner's refund claims for unutilized input tax credit were rejected by the Original Authority and Appellate Authority on the ground that the output supply was partially exempt.

Previous Decisions

The Original Authority (Assistant Commissioner) rejected the refund claims; the Appellate Authority (Joint Commissioner) upheld the rejection via Order-in-Appeal No.SG/JC/GST/189-195/RGD/APP/23-24 dated 31.10.2023.

Issues

Whether the refund of accumulated input tax credit under inverted duty structure is admissible under Section 54(3)(ii) of the CGST Act, 2017 when the output supply is partially exempt? Whether the formula under Rule 89(5) of the CGST Rules, 2017 was correctly applied by the authorities in computing the refundable amount?

Submissions/Arguments

The petitioner argued that the authorities misinterpreted Section 54(3)(ii) and Rule 89(5), and that the refund is clearly admissible even if the output supply is partially exempt. The respondents contended that the output supply being partially exempt disentitled the petitioner to refund, and that the rejection was proper.

Ratio Decidendi

The ratio decidendi is that the refund of accumulated input tax credit under inverted duty structure under Section 54(3)(ii) of the CGST Act, 2017 is admissible even if the output supply is partially exempt, and the formula under Rule 89(5) of the CGST Rules, 2017 must be applied correctly, including all relevant supplies in the 'Adjusted Total Turnover' and correctly computing 'Net ITC'.

Judgment Excerpts

The Petitioner in this petition under Article 226 of the Constitution of India is aggrieved by the rejection of refund claims for the accumulated tax credit due to inverted tax structure concurrently by the Original Authority as also in appeal by the Appellate Authority. The court held that the refund is admissible under Section 54(3)(ii) even if the output supply is partially exempt, and that the formula under Rule 89(5) must be applied correctly.

Procedural History

The petitioner filed refund claims for periods July 2017 to March 2018 and April 2018 to June 2018. The Original Authority rejected the claims. The petitioner appealed to the Appellate Authority, which upheld the rejection via Order-in-Appeal dated 31.10.2023. The petitioner then filed the present writ petition under Article 226 before the Bombay High Court.

Acts & Sections

  • Central Goods and Services Tax Act, 2017: Section 54(3)(ii)
  • Central Goods and Services Tax Rules, 2017: Rule 89(5)
  • Constitution of India: Article 226
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