Refund of integrated tax paid on goods or services exported out of India
Rule 96 of the CGST Rules
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Export with payment of IGST: the shipping bill itself is the refund application, and the refund is transmitted by the portal to Customs once GSTR-1 and GSTR-3B are filed and the data matches ICEGATE. The refund can be withheld where the exporter is flagged as risky or where an inquiry is pending, and it is not available where the inputs were procured under a concessional or deemed-export notification.
What this means in practice
The parts that actually decide cases — the things a practitioner checks first.
Rule 96(10), which barred the paid-IGST refund where inputs were imported under a concessional or advance-authorisation notification, was OMITTED from 08-10-2024 – but it still governs earlier periods, and demands for those years continue.
The refund flows automatically from the shipping bill once GSTR-1 and GSTR-3B match the ICEGATE data – most delays are data mismatches, not sanctions.
How this provision is built
The skeleton, clause by clause — useful when a notice cites a specific sub-clause.
The exact words of the law
5,629 characters, uneditedReproduced from the CBIC text. We explain it above — but you should always be able to read it yourself.
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(1) The shipping bill filed by 2 [an exporter of goods] shall be deemed to be an application n for refund of integrated tax paid on the goods exported out of India and such application shall be deemed to have been filed only when:-
(a) the person in charge of the conveyance carrying the export goods duly files 3 [a departure manifest or] an export manifest or an export report covering the number and the date of shipping bills or bills of export; and
(b) 4 [the applicant has furnished a valid return in FORM GSTR-3B : Provided that if there is any mismatch between the data furnished by the exporter of goods in Shipping Bill and those furnished in statement of outward supplies in FORM GSTR-1 18 [, as amended in FORM GSTR-1A if any,], such application for refund of integrated tax paid on the goods exported out of India shall be deemed to have been filed on such date when such mismatch in respect of the said shipping bill is rectified by the exporter;] 16 [
(c) the applicant has undergone Aadhaar authentication in the manner provided in rule 10B;] 17 [ Provided that the exporter of goods may file an application electronically in FORM GST RFD-01 through the common portal for refund of additional integrated tax paid on account of upward revision in price of goods subsequent to export of such goods, and on which the amount of integrated tax paid at the time of export of such goods has already been refunded in accordance with provisions of sub-rule
(3) of this rule, and such application shall be dealt with in accordance with the provisions of rule 89.]
(2) The details of the 5 [relevant export invoices in respect of export of goods] contained in FORM GSTR-1 shall be transmitted electronically by the common portal to the system designated by the Customs and the said system shall electronically transmit to the common portal, a confirmation that the goods covered by the said invoices have been exported out of India. 6 [****]
(3) Upon the receipt of the information regarding the furnishing of a valid return in 7 [ FORM GSTR-3B ] from the common portal, 8 [the system designated by the Customs or the proper officer of Customs, as the case may be, shall process the claim of refund in respect of export of goods] and an amount equal to the integrated tax paid in respect of each shipping bill or bill of export shall be electronically credited to the bank account of the applicant mentioned in his registration particulars and as intimated to the Customs authorities.
(4) The claim for refund shall be withheld where,-
(a) a request has been received from the jurisdictional Commissioner of central tax, State tax or Union territory tax to withhold the payment of refund due to the person claiming refund in accordance with the provisions of sub-section
(10) or sub-section
(11) of section 54 ; or
(b) the proper officer of Customs determines that the goods were exported in violation of the provisions of the Customs Act, 9 [ 1962; or] 10 [
(c) the Commissioner in the Board or an officer authorised by the Board, on the basis of data analysis and risk parameters, is of the opinion that verification of credentials of the exporter, including the availment of ITC by the exporter, is considered essential before grant of refund, in order to safeguard the interest of revenue.]
(5) 11 [***] 10 [(5A) Where refund is withheld in accordance with the provisions of clause
(a) or clause
(c) of sub-rule (4), such claim shall be transmitted to the proper officer of Central tax, State tax or Union territory tax, as the case may be, electronically through the common portal in a system generated FORM GST RFD-01 and the intimation of such transmission shall also be sent to the exporter electronically through the common portal, and notwithstanding anything to the contrary contained in any other rule, the said system generated form shall be deemed to be the application for refund in such cases and shall be deemed to have been filed on the date of such transmission. (5B) Where refund is withheld in accordance with the provisions of clause
(b) of sub-rule
(4) and the proper officer of the Customs passes an order that the goods have been exported in violation of the provisions of the Customs Act, 1962 (52 of 1962), then, such claim shall be transmitted to the proper officer of Central tax, State tax or Union territory tax, as the case may be, electronically through the common portal in a system generated FORM GST RFD-01 and the intimation of such transmission shall also be sent to the exporter electronically through the common portal, and notwithstanding anything to the contrary contained in any other rule, the said system generated form shall be deemed to be the application for refund in such cases and shall be deemed to have been filed on the date of such transmission. (5C) The application for refund in FORM GST RFD-01 transmitted electronically through the common portal in terms of sub-rules (5A) and (5B) shall be dealt in accordance with the provisions of rule 89.]
(6) 12 [***]
(7) 13 [***]
(8) The Central Government may pay refund of the integrated tax to the Government of Bhutan on the exports to Bhutan for such class of goods as may be notified in this behalf and where such refund is paid to the Government of Bhutan, the exporter shall not be paid any refund of the integrated tax. 14 [
(9) The application for refund of integrated tax paid on the services exported out of India shall be filed in FORM GST RFD-01 and shall be dealt with in accordance with the provisions of rule 89 ] 18 [****]
What changed, and when
The amendment trail, newest first — because the version that applies to your case depends on the period.
2024-10-08 · Omitted
20/2024-CTdated08
Omitted vide Notification No. 20/2024-CT dated 08.10.2024.
2024-07-10 · Inserted
12/2024-CTdated10
Inserted vide Notification No. 12/2024-CT dated 10.07.2024.
2023-08-04 · Omitted
38/2023-CTdated
Omitted vide Notification No. 38/2023 – CT dated 04.08.2023 for " Provided that where the date for furnishing the details of outward supplies in FORM GSTR-1 for a tax period has been extended in exercise of the powers conferred under section 37 of the Act, the supplier shall furnish the information
2022-10-01 · Substituted
Substituted (w.e.f. 01.10.2022) vide Notification No. 19_2022 – CT , dated 28.09.2022.
2022-01-01 · Inserted
35/2021-CTdated24
Inserted vide Notification No. 35/2021-CT dated 24.09.2021. Brought into force w.e.f. 01.01.2022 vide Notification No. 38/2021-C.T. , dated 21.12.2021.
2018-12-31 · Inserted
74/2018-CTdated31
Inserted vide Notification No. 74/2018-CT dated 31.12.2018.
2018-10-09 · Substituted
54/2018-CTdated09
Substituted vide Notification No. 54/2018-CT dated 09.10.2018 for: "(10) The persons claiming refund of integrated tax paid on exports of goods or services should not have received supplies on which the supplier has availed the benefit of the Government of India, Ministry of Finance, notification No
2017-10-23 · Inserted
75/2017-CTdated29
Inserted (w.e.f. 23.10.2017) vide Notification No. 75/2017-CT dated 29.12.2017.
2017-10-23 · Substituted
03/2018-CTdated23
Substituted for the words "an exporter" w.e.f. 23.10.2017 vide Notification No. 03/2018-CT dated 23.01.2018.
2017-10-23 · Substituted
03/2018-CTdated23
Substituted for the words "relevant export invoices" w.e.f. 23.10.2017 vide Notification No. 03/2018-CT dated 23.01.2018.
2017-10-23 · Substituted
03/2018-CTdated23
Substituted for the words "the system designated by the Customs shall process the claim for refund" w.e.f. 23.10.2017 vide Notification No.03/2018-CT dated 23.01.2018.
2017-10-23 · Substituted
3/2018-CTDated23
Substituted vide Notification No. 3/2018-CT Dated 23-01-2018, w.e.f. 23rd October, 2017 for [(9) The persons claiming refund of integrated tax paid on export of goods or services should not have received supplies on which the supplier has availed the benefit of notification No. 48/2017-Central Tax d
2017-07-01 · Substituted
14/2022-CTdated05
Substituted for the words " the applicant has furnished a valid return in FORM GSTR-3 or FORM GSTR-3B , as the case may be " w.e.f. 01.07.2017 vide Notification No. 14/2022-CT dated 05.07.2022.
2017-07-01 · Substituted
14/2022-CTdated05
Substituted for the figures " 1962 " w.e.f. 01.07.2017 vide Notification No. 14/2022-CT dated 05.07.2022.
2017-07-01 · Inserted
14/2022-CTdated
Inserted(w.e.f. 01.07.2017) vide Notification No.14/2022 – CT dated 05.07.2022.
2017-07-01 · Omitted
14/2022-CTdated05
Omitted(w.e.f. 01.07.2017) vide Notification No. 14/2022-CT dated 05.07.2022. Before it was read as " Where refund is withheld in accordance with the provisions of clause (a) of sub-rule (4), the proper officer of integrated tax at the Customs station shall intimate the applicant and the jurisdictio
2017-07-01 · Omitted
14/2022-CTdated05
Omitted(w.e.f. 01.07.2017) vide Notification No. 14/2022-CT dated 05.07.2022. Before it was read as " Upon transmission of the intimation under sub-rule (5), the proper officer of central tax or State tax or Union territory tax, as the case may be, shall pass an order in Part A of FORM GST RFD-07 ."
2017-07-01 · Omitted
14/2022-CTdated05
Omitted(w.e.f. 01.07.2017) vide Notification No. 14/2022-CT dated 05.07.2022. Before it was read as " Where the applicant becomes entitled to refund of the amount withheld under clause (a) of sub-rule (4), the concerned jurisdictional officer of central tax, State tax or Union territory tax, as the
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Text reproduced from the Central Board of Indirect Taxes and Customs, as available on 2026-09-05. The explanation and practice notes above are GSTZone’s own, written for this hub. If you spot anything out of date, tell us and we’ll fix it — this hub is checked daily against CBIC.
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