GST Amnesty Scheme 2026: Filing Steps Student Guide

Why This Matters Before You Even Open the GST Portal

Picture this: you are helping a relative or internship client, and you discover their GSTR-3B filings from 2017–18 or 2018–19 are still pending. The late fee alone — ₹200 per day (₹100 CGST + ₹100 SGST) — has been ticking for years. Without an amnesty window, that number is painful enough to make someone just give up and stay non-compliant forever.

That is exactly the problem the GST Amnesty Scheme 2026 is designed to solve. The government periodically issues notifications under the CGST Act that cap or waive late fees for past defaults, giving taxpayers a time-bound window to regularise without the full penalty burden. As a student, understanding this scheme is not just exam theory — it is the kind of practical knowledge that makes you genuinely useful on Day 1 of any accounting job.

This guide fills the gap most articles leave open: not just what the scheme is, but how you actually file under it, step by step, and what mistakes to avoid.

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What the GST Amnesty Scheme 2026 Notification Actually Says

Quick definition: A GST Amnesty Scheme is a time-limited government notification under the Central Goods and Services Tax (CGST) Act, 2017, that reduces or waives late fees for returns that were filed late or not filed at all.

The 2026 notification — issued by the CBIC (Central Board of Indirect Taxes and Customs) and available on the official portal at cbic-gst.gov.in — follows a pattern established by earlier amnesty rounds in 2021 and 2023. While you should always verify the exact notification number on the CBIC portal the day you advise a client (notifications get amended), the core structure is consistent:

Return Type	Period Covered	Capped Late Fee (per return)
GSTR-3B (nil returns)	Specified past quarters	₹500 (₹250 CGST + ₹250 SGST)
GSTR-3B (non-nil returns)	Specified past quarters	₹1,000 (₹500 CGST + ₹500 SGST)
GSTR-10 (final return)	Pending cases	₹1,000 (₹500 CGST + ₹500 SGST)
GSTR-4 (composition dealers)	Specified past years	₹500 per return

Important: The amnesty window is time-bound. Once the deadline passes, the scheme lapses and the full statutory late fee under Section 47 of the CGST Act applies again. Check cbic-gst.gov.in for the exact cut-off date of the current 2026 notification.

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Who Is Eligible — and Who Needs to Check Twice

Eligibility is simpler than most people assume, but there are traps.

You ARE eligible if:

• Your GSTR-3B, GSTR-10, or GSTR-4 for the specified periods is pending (not yet filed)
• You file the overdue return within the amnesty window
• You pay any outstanding tax liability along with the capped late fee

You are NOT covered if:

• You already paid the full (uncapped) late fee before the notification date — refunds on fees already paid are generally not provided under these schemes
• Your return falls outside the specified period mentioned in the notification
• You are under investigation or audit where dues are disputed (seek professional advice in that case)

Students: watch this exam trap. Examiners often ask whether the interest on late tax payment is also waived under amnesty. The answer is usually no — interest under Section 50 of the CGST Act (currently 18% per annum) is separate from the late fee under Section 47, and amnesty notifications typically address only the late fee component. Tax and interest must still be paid in full.

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Step-by-Step: How to Actually File Under the GST Amnesty Scheme 2026

Here is the practical walkthrough. I will use GSTR-3B as the example since it is the most common case.

Step 1 — Log in to the GST Portal Go to gstin.gov.in, click Login, and enter the taxpayer's GSTIN credentials.

Step 2 — Navigate to Returns Dashboard From the dashboard, go to Services → Returns → Returns Dashboard. Select the financial year and tax period for the pending return.

Step 3 — Prepare the GSTR-3B Click on GSTR-3B for the relevant period. Fill in:

• Table 3.1: Outward supplies and tax payable
• Table 4: Eligible ITC (Input Tax Credit)
• Table 5: Exempt, nil-rated, and non-GST outward supplies
• Table 6.1: Payment of tax

Worked mini-example: Suppose a small trader in Delhi has a pending GSTR-3B for July 2019. Tax liability is ₹8,000 (CGST ₹4,000 + SGST ₹4,000). Under the amnesty scheme, the late fee is capped at ₹1,000 (₹500 CGST + ₹500 SGST) instead of, say, ₹36,000 that would have accumulated at ₹200/day over ~180 days.

They pay: ₹8,000 (tax) + interest at 18% p.a. on ₹8,000 for the delayed period + ₹1,000 (capped late fee). The interest portion is non-negotiable.

Step 4 — Generate the Challan (PMT-06) Go to Services → Payments → Create Challan. Enter the amounts under the correct heads — CGST, SGST/UTGST, IGST, and CESS as applicable. Select your preferred payment mode (net banking, NEFT/RTGS, or over-the-counter at authorised banks).

Step 5 — Make Payment and Get CIN After payment, you receive a Challan Identification Number (CIN). The payment reflects in the Electronic Cash Ledger within 24 hours (usually much faster for online payments).

Step 6 — File the Return with DSC or EVC Return to the GSTR-3B draft. The system will auto-populate the late fee at the reduced/capped amount once the amnesty period is active. Verify, then file using either:

• DSC (Digital Signature Certificate) — mandatory for companies
• EVC (Electronic Verification Code sent to registered mobile/email) — allowed for other taxpayers

Step 7 — Download the Filed Acknowledgement (ARN) After successful filing, an Application Reference Number (ARN) is generated. Download and save the acknowledgement. This is your proof of compliance.

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Common Mistakes Students (and Junior Accountants) Make

Learning from errors before you make them is half the battle.

1. Filing the wrong period. The amnesty covers specific periods listed in the notification. Filing a return for a period outside that window will not get you the capped fee — you will be charged the full amount. Always cross-check the notification on cbic-gst.gov.in before proceeding.

2. Ignoring interest. As covered above, Section 50 interest is not waived. Forgetting to calculate and pay interest means the return may be technically filed but the tax ledger still shows dues.

3. Using the wrong challan head. Late fees must be paid under the Fee head, not the Tax head. Paying late fees under the tax head creates a mismatch that requires rectification — wasted time, panicked client call.

4. Missing the filing deadline. The amnesty window is usually 2–4 months. Missing it means the system reverts to full late fees. Set a calendar reminder the day you read the notification.

5. Confusing GSTR-3B amnesty with GSTR-9 amnesty. Different notifications cover different return types. Check which return is actually overdue before assuming coverage.

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How This Fits Into Your CA Inter / B.Com Exam Prep

GST late fees, interest, and amnesty schemes appear regularly in CA Inter Indirect Tax and B.Com Taxation papers. Examiners like to test:

• The distinction between late fee (Section 47) and interest (Section 50)
• The maximum late fee caps even outside amnesty (Section 47 was amended to cap fees at ₹10,000 per return for most taxpayers under the CGST Amendment Act)
• Numerical problems asking you to compute total dues for a late-filed return

If you want to drill these numericals under timed conditions alongside peers, the SuperAccountant cohort programme runs live problem-solving sessions specifically on Indirect Tax topics like this one — worth checking out if you are in your final months before exams.

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Quick-Reference Checklist Before You Hit "File"

Use this every time you help someone file under an amnesty scheme:

• Confirmed the return period is covered by the current notification (checked on cbic-gst.gov.in)
• Tax liability computed correctly in Table 3.1
• ITC claimed only if valid under Section 16(2) conditions
• Interest calculated at 18% p.a. on net tax liability from due date to payment date
• Late fee challan created under the Fee head (not Tax head)
• Payment confirmed and CIN noted
• Return filed within the amnesty window deadline
• ARN downloaded and saved

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The Bottom Line

The GST Amnesty Scheme 2026 notification is not complicated once you strip away the jargon. It is a capped late fee for overdue returns, filed through the standard GST portal workflow, with interest still payable in full. The value is enormous for small businesses carrying years of pending compliance — and your ability to walk a client through this process confidently is exactly what separates a useful junior accountant from someone who just knows the textbook.

Bookmark cbic-gst.gov.in for the current notification number and deadline. Do the walkthrough above on a test GSTIN if your college provides practice portal access. And make sure you understand the Section 47 vs Section 50 distinction cold — it comes up in exams more than almost any other late-fee question.

If you're not sure where to start, take SuperAccountant's free 10-minute quiz at https://app.superaccountant.in/en/quiz — it places you at the exact phase of our curriculum that matches your current level, so you stop revising what you already know.