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How to Claim a GST Refund on Exports With Payment of IGST

How to claim a GST refund on exports made with payment of IGST — the shipping bill acts as the refund application and IGST is refunded automatically once GSTR-1 and GSTR-3B are...

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GST
Published
August 25, 2026
Last updated
Oct 2, 2026
Reading time
4 min
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Last updated: October 2026Applies to: FY 2026-27Verified against: Government sources

Overview

Exports are "zero-rated" supplies. An exporter can either export on payment of IGST and claim the tax back, or export without payment under an LUT and claim unutilised ITC. This guide covers the first, "with payment of IGST" route, where the refund is largely automatic.

When It Is Required & Legal Basis

Section 16 of the IGST Act, 2017 makes exports zero-rated, and Section 54 of the CGST Act, 2017 with Rule 96 of the CGST Rules, 2017 governs the refund of IGST paid on export of goods. The shipping bill filed by the exporter is deemed to be an application for refund of the integrated tax paid.

Step-by-Step Process

  1. Pay IGST on the export invoice. Raise a tax invoice charging IGST and pay it through GSTR-3B.
  2. File the shipping bill. Ensure IEC, GSTIN, port code and invoice details on the shipping bill match the tax invoice.
  3. File GSTR-1 Table 6A. Report the export invoices with shipping bill number, date and port code.
  4. File GSTR-3B. Disclose the export turnover and IGST paid; total IGST paid must reconcile with GSTR-1.
  5. EGM filing by the carrier. The shipping line files the Export General Manifest confirming the goods have left India.
  6. Automatic credit. ICEGATE matches the data and credits IGST to the bank account linked to the IEC.

Forms, Attachments & Fees

DocumentRole
Shipping billDeemed refund application (Rule 96)
GSTR-1 Table 6AExport invoice reporting
GSTR-3BPayment of IGST on exports
EGMProof of export (filed by carrier)

No government fee. The bank account must be validated with customs (ICEGATE) for the IEC.

Timeline & Due Dates

Once GSTR-1, GSTR-3B and the EGM are in place and matched, refunds are typically processed within a few weeks. The outer limit under Section 54 is two years from the relevant date, but delays are usually caused by data mismatches rather than the time limit.

Penalty for Delay / Non-compliance

There is no penalty as such, but incorrect or excess IGST refund claimed is recoverable with interest under Section 50. Persistent mismatches can flag the exporter as risky and route refunds to manual scrutiny by customs.

Practical Tips

  • Match invoice value, GSTIN and port code exactly across the tax invoice, GSTR-1 and shipping bill.
  • File GSTR-3B on time — a delayed 3B holds the entire IGST refund.
  • Validate your IEC-linked bank account on ICEGATE; wrong bank details are a top rejection reason.
  • For export of services with IGST paid, this route does not apply — file RFD-01 instead.

Related Services & Guides

Quick recapKey facts & short answers

Key Facts About Claim a GST Refund

  • Applies in: All states across India, under the relevant central law.
  • Mode: Mostly online via the official government portal.
  • Typical timeline: Ranges from a few days to a few weeks depending on the case.
  • Non-compliance: May attract penalties, interest or late fees.
  • Expert help: TaxClue completes the entire process end to end for you.

How is IGST refunded on exports with payment of tax?

The shipping bill itself is treated as the refund application. Once the export manifest (EGM) is filed and GSTR-1 (Table 6A) and GSTR-3B data match on ICEGATE, IGST is credited to your bank account automatically — no separate RFD-01 is filed.

Do I need to file RFD-01 for IGST-paid exports?

No. For goods exported on payment of IGST, RFD-01 is not required; the refund flows through the customs system under Rule 96. RFD-01 is used for the without-payment (LUT) route.

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— TaxClue Compliance Desk

Claim a GST Refund: a key compliance topic in Indian tax and corporate law that businesses and individuals must understand to remain compliant.

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Vikas Sharma Verified expert Tax & Compliance Expert

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Last reviewed: Live

Disclaimer: This article is for general informational purposes only and does not constitute professional tax, legal or financial advice. Laws, rates and due dates change and can vary by individual case — always verify with the relevant government source (e.g. mca.gov.in, incometax.gov.in) or consult a qualified professional before acting. TaxClue accepts no liability for decisions taken based on this content.

People also ask

Questions, answered

Short, direct answers to the 6 questions readers ask most on this topic.

The shipping bill itself is treated as the refund application. Once the export manifest (EGM) is filed and GSTR-1 (Table 6A) and GSTR-3B data match on ICEGATE, IGST is credited to your bank account automatically — no separate RFD-01 is filed.

No. For goods exported on payment of IGST, RFD-01 is not required; the refund flows through the customs system under Rule 96. RFD-01 is used for the without-payment (LUT) route.

Mismatch between shipping bill and GSTR-1 invoice/value, non-filing or late filing of GSTR-3B, missing or wrong bank account/IEC details, or the EGM not being filed by the shipping line.

The general limit under Section 54 is two years from the relevant date, but since the refund is automatic on the shipping bill, timely and correct GSTR-1/3B filing is what matters most.

You should choose one route consistently. If IGST was paid, the with-payment route applies; mismatches between the LUT declaration and actual payment cause the refund to be held.

For IGST-paid goods exports, no portal refund application is filed; the exporter only ensures GSTR-1 Table 6A and GSTR-3B are correctly filed. Service exporters with IGST paid do file RFD-01.