Case Law Details
Agriex & Anr Vs Union of India & Anr (Gujarat High Court)
Material Facts
The petitioner-company filed an application on 15.12.2023 seeking refund of ₹1,63,70,582 towards Integrated Goods and Services Tax (IGST) paid on exports covered by shipping bills dated 08.05.2023 to 17.07.2023. Alternatively, it sought amendment of the shipping bills to reflect payment of IGST instead of exports under Letter of Undertaking (LUT), if required for processing the refund.
The respondents did not dispute that the goods had been exported. The exported goods were rice (pre-packaged and labelled), falling under Chapter Heading 1006 of Notification No. 1/2017-Integrated Tax (Rate) dated 28.06.2017, attracting 5% IGST. The petitioner stated that omission to mention IGST in the shipping bills was an inadvertent error.
Procedural History
A show cause notice dated 29.12.2023 was issued under Section 149 of the Customs Act, 1962. By order dated 22.02.2024, the Customs authorities rejected the refund application, holding that the invoices had been amended from LUT to IGST paid after export and that no documentary evidence existed at the time of export to permit amendment under Section 149.
Legal Issues
- Whether the refund application ought to be considered under Rule 96 of the CGST Rules, 2017.
- Whether rejection based on Section 149 of the Customs Act alone was justified.
Relevant Statutory Provisions
- Section 149 of the Customs Act, 1962.
- Rule 96, particularly sub-rule (4), of the CGST Rules, 2017.
- Notification No. 1/2017-Integrated Tax (Rate) dated 28.06.2017.
Court’s Findings and Reasoning
The Court observed that the Customs authorities considered only the request for amendment under Section 149 of the Customs Act and did not apply their mind to the petitioner’s principal prayer seeking refund of IGST.
The Court referred to Rule 96 of the CGST Rules, particularly Rule 96(4), which specifies three situations in which refund may be withheld. It noted that the petitioner’s case did not fall within any of those situations. The respondents also did not dispute that the goods had actually been exported and that the export invoices were on record.
The Court recorded that the authorities failed to examine the refund claim under Rule 96, which specifically provides for refund of integrated tax paid on exports.
The Court also noted that this legal position had been clarified in Amit Cotton Industries v. Principal Commissioner of Customs, (2019) 68 GSTR 226 and subsequently followed in Special Civil Application No. 2507 of 2023 decided on 14.08.2025.
Final Ruling
Without deciding the issue relating to amendment under Section 149 of the Customs Act, the Gujarat High Court directed the respondents to process the petitioner’s IGST refund under Rule 96 of the CGST Rules, observing that the case did not fall within Rule 96(4). The Court directed that a necessary order be passed by the next date of hearing, subject to further orders of the Court. The matter was kept on 17.07.2026.
FULL TEXT OF THE JUDGMENT/ORDER OF GUJARAT HIGH COURT
1. 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 petitioner-Company 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, (2019) 68 GSTR 226, which is also followed subsequently by the Coordinate Bench of this Court in 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.
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