How is the IGST refund amount calculated by GST officer with respect to Export of goods

Export of goods is a zero-rated supply under GST. This means tax is not meant to stay as a cost on exports. An exporter can take refund under two routes.

One route is export under LUT/Bond without payment of IGST and claim refund of unutilised input tax credit. The other route is export on payment of IGST and claim refund of the IGST paid.

This article will see export on payment of IGST and refund of IGST paid. After the legal change that took effect from 01 October 2023, export on payment of IGST is allowed only for the class of persons and class of goods or services notified under Section 16(4) of the IGST Act.

So, before looking at the refund amount, the exporter must confirm that the export on payment of IGST falls within the notified scope for that period. Once this route is valid, the refund amount follows a clear logic: the refund tracks the IGST that the exporter paid on export invoices that are linked to a shipping bill, subject to caps, matching rules, and legal bars.

2) Who processes the refund and when the GST officer steps in

For export of goods with payment of IGST, the refund is linked to the shipping bill under Customs. Under the GST framework, the shipping bill works as the refund application after the export gets confirmed and the return conditions are met.

In many exports, the refund flows through data exchange between GST and Customs systems. The GST officer enters the process in defined situations, such as these:

• The refund gets held back under the rule framework and the claim moves to the GST side for processing through the refund workflow.
• The exporter pays additional IGST after export due to an upward price revision and files FORM GST RFD-01 to claim refund of that extra IGST.

So, the refund amount has two layers of work:

1. A system layer that reads shipping bill and return data and forms the base refund figure.
2. An officer layer where the GST officer checks eligibility, checks tax payment, applies caps, and passes an order for sanction or rejection when the claim reaches the GST office.

3) The core idea: refund equals IGST paid on export invoices linked to the shipping bill

In this route, the refund is tied to export invoices that carry IGST and are reported as export with payment of tax. The exporter reports these export invoice details in GSTR-1 Table 6A with shipping bill number and date. If the exporter makes corrections through GSTR-1A, those amended details also matter for matching.

The exporter also files GSTR-3B for the tax period and pays the IGST liability. The refund amount starts from this base:

IGST refund for a shipping bill = total IGST on export invoices mapped to that shipping bill

This base amount moves forward only when the data matches and the legal conditions permit the refund.

4) Step-by-step: how the refund amount is worked out from records

Step A: Compute IGST on each export invoice

For each export invoice under this route, IGST is computed as:

IGST on invoice = taxable value × IGST rate

Example: taxable value ₹10,00,000 at 18% gives IGST ₹1,80,000.

That IGST amount must appear in the export invoice, must be reported in GSTR-1 Table 6A, and must form part of the IGST liability paid through GSTR-3B.

Step B: Add invoice IGST shipping bill-wise

Refund is processed shipping bill-wise. A shipping bill can include one export invoice or more than one export invoice. The IGST for that shipping bill becomes the sum of IGST on all export invoices linked to it.

So the working number is:

IGST for shipping bill = IGST of invoice 1 + IGST of invoice 2 + …

This is the first stage of the refund amount.

Step C: Confirm export and return conditions under Rule 96

The shipping bill works as a refund application after key conditions are met. These conditions include export confirmation through the export manifest or export report and filing of a valid GSTR-3B. Rule 96 also brings in Aadhaar authentication under Rule 10B where required.

If the export confirmation is not in place, the refund does not move.

Step D: Matching check between shipping bill data and GSTR-1 (and GSTR-1A, if filed)

A major part of the process is matching. The core matching points include invoice number, invoice date, taxable value, IGST amount, shipping bill number, shipping bill date, and port code. If there is mismatch between the shipping bill and GSTR-1 export data, the refund does not move until the mismatch is corrected. If corrections are filed through GSTR-1A, those corrected values become relevant for matching.

This step affects timing, and it can also affect the amount when the IGST figure in the records changes due to correction.

Step E: Apply the “tax paid cap” from GSTR-3B (Table 3.1(b))

This step controls how much refund can be granted for a period.

A key validation is the relation between:

• IGST claimed on export invoices in GSTR-1 Table 6A, and
• IGST paid in GSTR-3B Table 3.1(b).

If IGST paid in GSTR-3B Table 3.1(b) is less than the IGST claimed in GSTR-1 Table 6A for that period, the refund gets restricted to the IGST paid figure.

So the cap reads like this:

Permissible IGST refund for the period ≤ IGST paid in GSTR-3B Table 3.1(b) for that period

Example:

• IGST on export invoices in GSTR-1 Table 6A: ₹1,80,000
• IGST paid in GSTR-3B Table 3.1(b): ₹1,50,000 Refund amount that survives this cap: ₹1,50,000, subject to shipping bill linkage and matching.

This cap prevents a refund for tax that is not paid through the return.

5) Legal checks that can reduce the refund to zero

Even if the invoice and return figures match and the cap is met, the law blocks refund in some cases.

A major bar is the export duty bar. If the exported goods are subject to export duty, Section 16(5) blocks refund of IGST paid on those goods. In such a case, the admissible refund becomes zero for that export, even if IGST was paid and reported.

6) What the GST officer checks when the claim reaches the GST office

When a refund claim reaches the GST officer due to withholding or due to an additional IGST claim after export, the officer checks record consistency and legal eligibility.

The officer checks export linkage: whether the export invoices in GSTR-1 Table 6A match the shipping bill and whether the export confirmation exists. The officer checks return compliance: whether GSTR-3B is filed and whether IGST payment for exports is reflected in Table 3.1(b). The officer checks the amount cap: whether the refund request crosses the Table 3.1(b) paid figure for the period. The officer checks the export duty bar: whether the goods fall under export duty.

The officer also checks for mismatch corrections through GSTR-1A where filed, since those corrections control the matching outcome.

7) Special case: refund of additional IGST paid after export due to price revision

Sometimes export price rises after export due to contract terms. In such a case, the exporter raises a supplementary document and pays additional IGST after export. The original IGST refund under the shipping bill route covers IGST paid at the time of export. For additional IGST paid after export, the exporter files FORM GST RFD-01 and the GST officer processes the claim.

The amount logic in this case is direct:

• Identify the additional IGST paid after export for the same exported goods.
• Ensure that IGST component was not refunded earlier under the shipping bill route.
• Sanction refund for the additional IGST that meets linkage and payment checks.

The officer checks linkage to the same export, checks proof of additional tax payment through returns, and checks that there is no duplicate refund for the same tax.

8) Note on Rule 96(10)

Rule 96(10) was omitted through a notification dated 08 October 2024. This change affects eligibility restrictions that were tied to that sub-rule. The core amount logic for IGST refund on export of goods stays based on invoice IGST, shipping bill linkage, matching rules, and the GSTR-3B Table 3.1(b) cap.

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