Harun Raaj & AssociatesHarun Raaj & Associates

GST Compliance Journey · Step 2 of 2

Registration & Filing
2Refunds
Indirect Tax Servicesvia GST Portal

GST Refund Services

GST Refund

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SCOPEConfirmed in writing
TYPICAL TIMELINE30 days
DOCS REQUIRED5 documents
APPLICABLE TOCompany, LLP, Partnership

Regulatory Framework

GST refunds are governed by Section 54 of the Central Goods and Services Tax (CGST) Act, 2017, read with Rule 89 of the CGST Rules, 2017.

Section 54(1) — Any person claiming a refund of tax, interest, or any other amount paid may apply in FORM RFD-01 electronically before the expiry of two years from the "relevant date." Explanation 2 to Section 54 defines the relevant date by category of claim — for export of goods, the date the ship/aircraft leaves India or the date the goods cross the border by land/post; for export of services, the date of receipt of payment in convertible foreign exchange (or the invoice date, if payment was received in advance); for a refund arising from an inverted duty structure, the end of the financial year in which the claim arises; and for tax paid by mistake, the date of payment.

Section 54(3) — Refund of unutilised Input Tax Credit is permitted only where the credit accumulation arises from: zero-rated supplies made without payment of tax (exports/SEZ supplies under a Letter of Undertaking), or an inverted duty structure where the tax rate on inputs exceeds the rate on the output supply.

Rule 89 — The refund application in FORM RFD-01 must be accompanied by supporting documents (invoices, shipping bills/export documents, the GSTR-2B statement) and, for claims exceeding ₹2 lakh, a certificate from a Chartered/Cost Accountant under Rule 89(2)(m) confirming that the incidence of tax has not been passed on to any other person.

Refunds not sanctioned within 60 days of a complete application attract interest under Section 56 of the CGST Act.

Overview

A GST refund claim is the recovery of tax that the business paid but should not have — unutilised input tax credit accumulated on zero-rated exports, refund of tax paid on the inverted duty structure under Section 54(3) of the CGST Act 2017, refund on deemed exports, or refund of excess tax paid. The mechanism is Section 54 of the CGST Act read with Rules 89 to 91 of the CGST Rules: the claim is filed in RFD-01 on the portal, and the department must sanction or reject it within the prescribed period, with the deficiency process under Rule 90 as the gateway.

The refund is the correction of the cash position. The credit that accumulates on exports and on the inverted duty structure is the business's own money sitting in the ledger, and the refund claim is how it comes back. The process has a discipline — the claim must match the ledger, the invoices and the export data, and every mismatch is a deficiency that restarts the clock.

The cost of an abandoned refund is the permanent cash loss: the unclaimed credit that stays blocked, the amounts that lapse because the claim was never filed or died in the deficiency cycle. For a business with export turnover or an inverted structure, the refund is not a windfall; it is the working capital the business is entitled to under the Act.

This service is for businesses with refundable positions — exporters, inverted-duty manufacturers, deemed-export suppliers. We compute the refundable amount under Section 54, prepare the RFD-01 with the ledger and invoice support, file and track the claim through the deficiency and sanction stages, and handle the rejection and the appeal where the department refuses.

How It Works

  1. 1

    Refund Position Computation

    We compute the refundable amount under Section 54 from the ledger and the turnover.

    Harun Raaj & Associates does this3-5 days
  2. 2

    Supporting Records

    We assemble the invoices, the export documents and the ledger statements.

    Harun Raaj & Associates does this1 week
  3. 3

    RFD-01 Filing

    We prepare and file the refund claim in RFD-01 on the portal.

    Harun Raaj & Associates does this1 week
  4. 4

    Deficiency & Sanction Tracking

    We respond to deficiencies under Rule 90 and track the sanction to payment.

    Harun Raaj & Associates does this2-8 weeks
  5. 5

    Rejection & Appeal

    We pursue the appeal where the claim is rejected or sanctioned short.

    Harun Raaj & Associates does thisAs required

Frequently Asked Questions

What are the main categories of GST refund available?
Section 54 CGST Act: (1) IGST paid on zero-rated exports — auto-processed via GSTR-1 and ICEGATE linkage; (2) ITC accumulated on zero-rated supplies (exports without IGST payment under LUT) — RFD-01 via Rule 89; (3) inverted duty structure (input GST rate > output GST rate) — RFD-01 under Section 54(3)(ii); (4) excess cash ledger balance — RFD-01 within 30 days; (5) tax paid in excess due to assessment order later set aside; (6) refund due to year-end reconciliation of TCS/TDS credits.
What is the time limit for filing a GST refund application?
2 years from the 'relevant date' under Rule 89(1). For exports: date of export (shipping bill date). For inverted duty structure: end of the financial year in which the claim arises. For excess payment: date of payment. Missing the 2-year window results in permanent forfeiture — there is no condonation provision under the CGST Act. Even a day's delay after 2 years is fatal — ensure applications are filed well within the deadline.
What is the inverted duty structure refund formula?
Rule 89(5): Refund = (Net ITC × Turnover of inverted-rated supplies) ÷ Adjusted Total Turnover. Net ITC excludes ITC on capital goods and exempt supplies. The Supreme Court in VKC Footsteps India (2021) confirmed that ITC on input services is excluded from Net ITC for the Rule 89(5) formula — only ITC on goods qualifies. This is a significant restriction for service-intensive manufacturers.
What is IGST refund on exports and why does it get stuck?
IGST export refund is auto-processed when: GSTR-1 shipping bill details match ICEGATE customs records. Common reasons for delay: (a) invoice amount, port, or GSTIN mismatch between GSTR-1 and ICEGATE; (b) EGM not filed by the shipping carrier; (c) GSTR-3B not filed for the period; (d) pending alert flags on the GSTIN (tax arrears, pending returns). Resolution: use the GSTN-ICEGATE refund status tool to identify the specific mismatch and resolve via the GSTN helpdesk or amendment.
What interest applies if the department delays a GST refund?
Section 56 CGST Act: if the refund application is not disposed of within 60 days from the date of receipt of the complete application, the department is liable to pay interest at 6% per annum. Interest accrues automatically — no separate request is needed. The refund + interest can be enforced through a writ petition if the department ignores the Section 56 obligation. Commissioner-level intervention may be required for large stuck refunds.

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