Rule 96: The Shipping Bill as a Refund Application

Rule 96 explained: this guide covers what it means, who it applies to, the step-by-step process, documents required, fees, due dates and penalties in India — so you can stay compliant with confidence and avoid costly mistakes.

For an exporter of goods paying IGST, there is no refund application to file. The shipping bill is the application — and it is deemed filed only when three separate things have happened, none of them in the exporter's sole control.

Rule 96(1): the shipping bill filed by an exporter of goods shall be deemed to be an application for refund of integrated tax paid on the goods exported out of India, and shall be deemed to have been filed only when — (a) the person in charge of the conveyance files a departure manifest or an export manifest or an export report covering the number and date of the shipping bills or bills of export; (b) the applicant has furnished a valid return in FORM GSTR-3B; and (c) the applicant has undergone Aadhaar authentication in the manner provided in Rule 10B.

The three conditions

(a) The manifest. Filed by the carrier, not the exporter. Until the EGM or departure manifest is filed and matched to the shipping bill, the refund does not begin. A mismatch here — wrong shipping bill number, wrong date — is the most common cause of a refund that never appears without any communication to the exporter.

(b) A valid GSTR-3B. The return for the period must be filed. Not GSTR-1 alone.

(c) Aadhaar authentication under Rule 10B. Added later, and applying to the registered person — for a company, the authentication of the specified persons under s.25(6C). A registration that never completed Aadhaar authentication cannot receive an export refund under this route. Biometric Aadhaar authentication →

The mismatch proviso

"Provided that if there is any mismatch between the data furnished by the exporter of goods in the Shipping Bill and those furnished in the statement of outward supplies in FORM GSTR-1, 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."

So a mismatch does not reject the claim — it postpones the filing date until the exporter fixes it.

That has two consequences:

Interest under s.56 runs from sixty days after the corrected filing date, not the original one. The exporter bears the delay.

The two-year limit in s.54(1) runs from the relevant date, and a long-uncorrected mismatch can push the deemed filing date past it.

What must match: the GSTIN, the shipping bill number and date, the port code, the invoice number and date, and the taxable value and IGST amount. Table 6A of GSTR-1 carries these, and they must agree with the shipping bill exactly.

Price revision after export

The proviso to Rule 96(1) as inserted: where the price of exported goods is revised upward after export, and IGST was already refunded on the original value, the exporter may file an application electronically in FORM GST RFD-01 for refund of the additional integrated tax paid, dealt with under Rule 89.

So an upward price revision moves out of the automatic shipping-bill route into the ordinary RFD-01 route. A downward revision engages Rule 96(10) territory and the recovery of excess refund.

Rule 96(4): withholding

The refund may be withheld where:

(a) a request has been received from the jurisdictional Commissioner to withhold payment of refund due to the person in view of s.54(10) or (11) — that is, defaults in furnishing returns or unpaid dues, or a pending appeal where the Commissioner is of the opinion that grant of refund is likely to adversely affect revenue on account of malfeasance or fraud; or

(b) the proper officer of Customs determines that the goods were exported in violation of the Customs Act, 1962.

Where a refund is withheld, the proper officer of integrated tax at the Customs station intimates the applicant and the jurisdictional Commissioner, and the matter is transmitted to the common portal in FORM GST RFD-01, to be dealt with under Rule 89 and Rule 92.

Who cannot use Rule 96

Rule 96(10) restricts the with-payment route. A supplier who has received supplies on which the benefit of specified notifications has been availed — advance authorisation, EPCG, EOU and specified deemed export notifications — is not entitled to claim refund of IGST paid on exports under this route.

The consequence for such an exporter is that it must use the LUT route and claim refund of unutilised credit under Rule 89(4) instead. Rule 96A: exports under LUT →

This restriction has produced a substantial body of litigation, and its scope should be checked against the current text before an exporter with advance authorisation chooses a route.

Key takeaways

• The shipping bill is the refund application for IGST-paid exports of goods.
• Deemed filed only on the manifest, a valid GSTR-3B, and Aadhaar authentication.
• A GSTR-1 to shipping bill mismatch postpones the filing date until rectified — and interest runs from the corrected date.
• Upward price revision after export goes through RFD-01 under Rule 89.
• The refund may be withheld on a Commissioner's request under s.54(10) or (11), or a Customs violation.
• Rule 96(10) bars the route for exporters who availed specified duty-free import benefits.

Read next

• Refund of IGST Paid on Exports: The Shipping Bill Route
• Rule 96A: LUT and the Fifteen-Day Consequence
• Rule 89(4): The Zero-Rated Refund Formula
• Rule 96B: Recovery Where Export Proceeds Are Not Realised

Disclaimer: Positions stated as on 5 September 2026, based on the CGST Rules as amended to 31 March 2026 (ICAI Bare Law, 12th edition) and the ICAI Handbook on Refunds under GST (January 2026).