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GST Refunds on Export Inputs: A CFO’s 2025 Compliance Playbook 📊✈️

Abhishek Raja Ram
Abhishek Raja Ram at June 06, 2025

GST Refunds on Export Inputs 2025 CFO

Exports remain zero-rated under India’s GST, yet the cash locked in input tax credit (ITC) can strain working capital if the refund process is inefficient. Below is a walkthrough—precise on law, practical for finance leaders—to ensure every rupee spent on export inputs makes its way back to your bank account.CFO's Compliance Playbook

Provision

Why it matters

Sec. 54 CGST Act

Governs all GST refunds, including the two-year filing clock.

Sec.16 IGST Act

Declares exports zero-rated, unlocking ITC refunds or IGST rebates.

Rule 89 CGST Rules

Lays down the forms, formulae and documentation (Statements 3, 3A, 9A, 9B).

Rule 89(1B)

Allows for a refund of the additional IGST paid later, as the export price increased. Inserted via Notification 12/2024-CT, 10 Jul 2024.

Rule 96A (amended)

Extends the time to realise export proceeds to FEMA timelines (no longer a 1-year limit).

Circular 226/20/2024-GST

Prescribes the documentary pack for refunds of additional Integrated Goods and Services Tax (IGST).

GSTN Advisory 14 Jul 2024

Temporary portal workaround—file under “Any other” until a dedicated category appears.

2. Two Pathways to Liquidate Your Tax Credit

Route

Cash-flow impact

What you actually claim

A. LUT / Bond (No IGST at port)

Neutral—no IGST blocked

Refund of unutilised ITC on inputs & input services via RFD-01

B. Pay IGST at Customs

Negative initially; refund automatically

Customs auto-credits basic IGST refund under Rule 96(3). Additional IGST due to later price hikes is reclaimed separately via RFD-01 (Rule 89(1B)).

3. Step-by-Step Road-Map (Route A: Unutilised ITC)

  1. House-keeping

    • File GSTR-1 & 3B for the period; reconcile with books and ICEGATE shipping data.

  2. LUT in place

    • Furnish/renew Letter of Undertaking (Form GST RFD-11) before export.

  3. Prepare RFD-01

    • Fill Statement 3A (turnover & ITC), auto-populate invoices from GSTR-1.

  4. Attach evidence

    • Shipping bills, export invoices, BRC/FIRC (services) or proof of export (goods), inward supply invoices, self-certified reconciliation of ITC.

  5. Debit ITC ledger equal to the claim.

  6. Track Deficiency Memo (RFD-03) and respond within 15 days to avoid fresh filing.

  7. Refund Order (RFD-06) & payment advice (RFD-05)—funds hit the bank via PFMS.

Time-limit – File within 2 years from the “relevant date”. Delay = forfeiture, unless the Commissioner condones under specific circulars.

4. Step-by-Step Road-Map (Route B: Additional IGST After Price Revision)

  1. Pay supplementary IGST

    • Issue debit note/supplementary invoice; discharge tax via GSTR-3B.

  2. File RFD-01 under “Any other” (until GSTN launches the new category).

  3. Upload Statements 9A & 9B with:

    • Original & supplementary invoice numbers

    • Shipping-bill details

    • Proof of extra remittance (FIRC/BRC)

    • Proof of additional IGST payment & CA/CMA certificate (Rule 89 (2)(bb),(bc)).

  4. The two-year clock runs from the date of the supplementary shipping bill/invoice, with a one-time grace period for older exports (Rule 89(1B) proviso).

  5. Processing by a jurisdictional GST officer (not Customs) as per Circular 226/20/2024. 

5. “Relevant Date” Decoder (for the two-year rule)

  • Sea/Air – Date vessel/aircraft leaves India.

  • Land – Date goods cross the frontier.

  • Post – Date of dispatch by post office.

  • Services (payment pre-export) – Invoice date.

  • Services (payment post-export) – Receipt date.

  • Deemed exports – Return filing date reporting the supply.

  • Price-revision IGST – Shipping-bill date of the supplementary invoice (Rule 89(1B)).

6. Exceptions & Extensions CFOs Should Exploit

Scenario

Relief

Payment for services not realised in 1 year

Commissioner may grant further time aligned to FEMA extensions.

Delayed exports (beyond LUT’s 3-month window)

Post-facto extension possible by Commissioner; notify via DRC-20.

Portal category missing

Use “Any other” with proper remarks until GSTN releases the new refund tile.

Amount < ₹1,000

Statutory de-minimis—no refund processed (s 54(14)).

7. Governance Checklist for Finance Leaders ✅

  1. One-click ITC tracker – Automate ledgers to flag ineligible or blocked credits (Rules 38, 42, 43).

  2. Shipping-bill ↔ Invoice mapping – Ensure ICEGATE & GSTR-1 data match; customs suspends refund for mismatches.

  3. Contract clauses – Capture price-revision terms upfront. Easier to justify additional IGST refunds.

  4. Document vault – Digitally store invoices, FIRCs, CA certificates; retention = 72 months (Sec. 36 CGST Act).

  5. Quarterly mock audit – Simulate refund scrutiny; identify gaps before GST authorities do.

  6. ERP patches – Enable LUT renewal alerts, Rule 89 Excel output, and auto-generation of Statements 9A/9B.

  7. Litigation watch – Track High-Court rulings on inverted duty refunds and export duty denial to strategise claims.

8. Common Pitfalls Triggering Refund Rejections 🚩

  • Availing drawback + ITC refund on the same goods.

  • Exporting goods that attract export duty (no ITC refund).

  • Failing to debit the electronic credit ledger when filing RFD-01.

  • Using ineligible credits (motor vehicles, personal consumption) in the refund formula.

  • Mismatched port codes or invoice values between GSTR-1 & shipping bill.

  • BRC/FIRC not reflecting full consideration for service exports.

9. Strategic Take-aways for CFOs

  1. Cash-flow Predictability – Treat refund lead-time as a KPI; escalate if RFD-06 exceeds 60 days.

  2. Policy Awareness – Notification 12/2024-CT now lets you claw back extra IGST—use it.

  3. Documentation Culture – The strongest defence in a refund audit is contemporaneous paperwork.

  4. Tech Integration – Invest in GST-ERP connectors that auto-populate RFD-01 and reconcile ICEGATE data.

  5. Continuous Learning – Refund rules shift fast; schedule quarterly trainings for your tax team.

Final Word

Export refunds are no longer a clerical task—they’re a strategic liquidity lever. Deploy the controls above, stay alert to 2024-25 rule changes, and you’ll maintain a healthy working capital position and keep regulators satisfied.

Do you have a specific scenario or sector-specific nuance? Drop a note, and I’ll break it down with case law and practical structuring tips.

About the Author

Abhishek Raja Ram

Abhishek Raja Ram

Senior Author

Abhishek Raja Ram - Popularly known as Revolutionary Raja; is FCA, DISA, Certificate Courses on – Valuation, Indirect Taxes , GST etc, M. Com (F&T) Mr. Abhishek Raja “Ram” is a Fellow member of Read more...

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