Undisputed Exporter Entitled to IGST Refund Under Rule 96 Despite Omission of Tax Details in Shipping Bills

By | July 15, 2026
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Undisputed Exporter Entitled to IGST Refund Under Rule 96 Despite Omission of Tax Details in Shipping Bills

Undisputed Exporter Entitled to IGST Refund Under Rule 96 Despite Omission of Tax Details in Shipping Bills

Issue

Whether an exporter can be denied an IGST refund under Rule 96 of the CGST Rules for undisputed exports simply because they inadvertently omitted the 5% IGST details in their shipping bills, and whether the revenue can condition this refund on a formal amendment of the shipping bills under Section 149 of the Customs Act.

Facts

  • The petitioner exported pre-packaged and labeled rice (falling under Tariff Heading 1006), which attracted a 5% IGST rate.

  • The petitioner filed a refund application before the Customs authorities for the IGST paid on these export consignments.

  • Due to an inadvertent error, the 5% IGST details were omitted from the specified shipping bills.

  • The tax department did not dispute the actual export of the goods, and all corresponding export invoices were fully available on record.

  • The Customs authority issued a notice regarding the amendment of the shipping bills under Section 149 of the Customs Act, but ultimately rejected the request to amend the status from Letter of Undertaking (LUT) to IGST, citing the “post-export change” and an alleged lack of contemporaneous evidence.

  • Consequently, the revenue authorities failed to examine the primary substance of the petitioner’s IGST refund claim.

Decision

  • Held, that the refund of integrated tax (IGST) on exports is strictly governed by Rule 96 of the CGST Rules, which provides a exhaustive and limited set of grounds under sub-rule (4) for withholding a refund.

  • Held, that since the petitioner’s case does not fall under any of the specified withholding contingencies in Rule 96(4), and the physical exports are entirely undisputed, a clerical omission of IGST details in the shipping bills cannot defeat their statutory refund entitlement.

  • Held, that the Customs authority’s decision to restrict its focus to the procedural amendment under Section 149 of the Customs Act is legally misconceived when the substantive criteria under Rule 96 of the CGST Rules stand fully satisfied.

  • Held, that the respondents are directed to process the petitioner’s IGST refund under Rule 96 immediately, without requiring any prior or separate adjudication on the shipping bill amendment under Section 149.

Key Takeaways

  • Substance Over Procedural Errors: Inadvertent clerical omissions or mistakes in shipping documents cannot block substantive export incentives and tax refunds when the physical export of goods is verified and undisputed.

  • Rule 96 is Self-Contained: The grounds for withholding an IGST refund under Rule 96(4) of the CGST Rules are exhaustive. If an exporter’s situation does not fit these specific legal exceptions, the revenue department has no authority to stall the refund on other administrative or procedural grounds.

  • No Linkage to Section 149 Customs Amendments: An IGST refund on export of goods cannot be made conditional upon the successful completion of a formal shipping bill amendment under Section 149 of the Customs Act, as long as the tax payment and physical export are proved by other contemporaneous records like invoices.

HIGH COURT OF GUJARAT
Agriex
v.
Union of India
A.S. Supehia and Ms. VAIBHAVI D. NANAVATI, JJ.
R/SPECIAL CIVIL APPLICATION NO. 5623 of 2024
JULY  2, 2026
Uchit N. Sheth for the Petitioner. Utkarsh R. Sharma for the Respondent.
ORDER
A.S. Supehia, J.- The petitioner-Company filed the application seeking refund on 15.12.2023 before the Deputy Commissioner of Customs with respect to the shipping bills for the period from 08.05.2023 to 17.07.2023 of Integrated Goods and Services Tax (IGST) paid on exports. The respondents have not disputed that the goods are exported by the petitioner-Company. The petitioner-Company, in the application made two prayers as under:
“9(a) Your goodself may be pleased to grant refund of IGST of Rs. 1,63, 70,582 which has been paid by us in respect of exports made through shipping bills for the period from 8.5.2023 to 17.7.2023.
(b) Without prejudice to the above and in the alternative and if so required for the purpose of granting refund, shipping bills filed for the period from 8.5.2023 to 17.5.2023 may please be allowed to be amended and tax paid by us under the IGST Act in respect of such export transactions may please be mentioned on the shipping bills after which such refund may be processed and released at the earliest;”
2. Thereafter, a show-cause notice was issued to the petitioner-Company by the respondent Customs authority on 29.12.2023 referring to the provisions of Section 149 of the Customs Act, 1962, calling upon for a personal hearing in relation to the claim of refund. Ultimately, by the order dated 22.02.2024, the Customs authorities have rejected the refund application by placing reliance on the provisions of Section 149 of the Customs Act and by stating that the petitioner amended the invoices from Letter of Undertaking (LUT) to IGST paid after the cargo was cleared or exported, and no documentary evidence was in existence at the time goods were cleared or exported; therefore, the amendment request from LUT to IGST paid under Section 149 of the Customs Act is rejected.
3. Thus, the respondent Officer did not apply his mind to prayer ‘9(a)’ made by the petitionerCompany in the refund application dated 15.12.2023 asking for refund of Rs.1,63,70,582/-, which was paid in respect of exports.
4. At this stage, it would be apposite to refer to the provisions of Rule 96 of the Central Goods and Services Tax (CGST) Rules, 2017 more particularly, sub-rule (4), which prescribes three eventualities under which the claim for refund can be withheld. The case of the petitioner does not fall in either of them.
5. The respondents have not disputed that the petitioners have actually exported the goods. The invoices relating to the exports are placed on record. The respondent thus, has examined the case of the petitioner-Company in context with the provisions of Section 149 of the Customs Act however, has failed to examine the case of the petitioner-Company under Rule 96 of the CGST Rules, wherein the refund of integrated tax paid on goods or services exported out of India, and the procedure for the same, is provided.
6. It is also not in dispute that the goods of the petitioner-Company, being Rice (pre-packaged and labeled), falls under Chapter heading 1006 of Notification No.1 of 2017-Integrated Tax (Rate) dated 28.06.2017, prescribing 5% of integrated tax, which was supposed to be mentioned in the shipping bills however, due to an inadvertent error, the petitioner could not do so.
7. Under these circumstances, we direct that the respondents shall process the refund of the petitioner under Rule 96 of the CGST Rules in wake of the undisputed fact that the case of the petitioner-Company does not fall within the provisions of sub-rule (4) of Rule 96 of the CGST Rules, which provides three eventualities in which the refund can be refused.
8. This position of law is already clarified by this Court in the judgment of Amit Cotton Industries v. Principal Commissioner of Customs 75 GST 33/29 GSTL 200 (Gujarat)/(2019) 68 GSTR 226, which is also followed subsequently by the Coordinate Bench of this Court in Ruhi Siraj Makda v. Union of India  Special Civil Application No.2507 of 2023, decided vide judgment dated 14.08.2025.
9. Thus, at this stage, without going into the issue of the amendment under Section 149 of the Customs Act, the refund of the petitioner-Company shall be processed. Necessary order shall be passed by the next date of hearing, which would be subject to further order passed by this Court.
The matter is kept on 17.07.2026.