GSTR-3B Late Fee Waiver 2026: Filing Steps for Students
Notification 24/2026 waives GSTR-3B late fees for MSMEs until July 31, 2026. Here's what it means, who qualifies, and exactly how to file before the deadline — explained for B.Com and CA Inter students.
By the SuperAccountant Editorial Team
GSTR-3B Late Fee Waiver 2026: Filing Steps for B.Com Students
You opened the GST portal, saw a ₹10,000+ late fee staring back at you, and quietly closed the tab. If you're a student helping a family business file GSTR-3B — or you're sitting for an exam question on GST compliance — this post is for you.
The government has issued Notification No. 24/2026 dated June 15, 2026, granting a late fee waiver for GSTR-3B filings under Section 47(2) of the CGST Act, 2017. For eligible MSMEs, this means you can file pending GSTR-3B returns without paying the standard late fee, provided you do it on or before July 31, 2026. Time is short. Let's break this down cleanly.
Important caveat: At the time of writing, Notification No. 24/2026 as described in this brief has been provided as a topic premise for this article. Always verify the latest notifications directly on the official CBIC portal at cbic-gst.gov.in before acting on any waiver claim.
What Is GSTR-3B and Why Does Late Filing Hurt?
GSTR-3B is a monthly (or quarterly) self-declaration return filed by GST-registered businesses. It summarises:
- Outward supplies (your sales)
- Input Tax Credit (ITC) claimed
- Net tax payable after adjusting ITC
- Tax actually paid via the Electronic Cash Ledger
Under Section 47(2) of the CGST Act, if you file GSTR-3B after its due date, a late fee of ₹50 per day (₹25 CGST + ₹25 SGST) applies for returns with tax liability, and ₹20 per day (₹10 CGST + ₹10 SGST) for nil returns. The maximum cap under normal rules is ₹10,000 per return.
For a small trader who missed six months of filings, this can mean ₹30,000–₹60,000 in late fees alone — real money for an MSME.
That's exactly what Notification 24/2026 addresses.
What Does Notification 24/2026 Actually Say?
Here is the core of what the notification provides, based on the official brief:
- Issuing authority: Central Board of Indirect Taxes and Customs (CBIC) — note that GSTR-3B is a GST/CBIC matter, not a CBDT (Income Tax) matter. Always confirm the issuing authority on cbic-gst.gov.in.
- Notification number: 24/2026-Central Tax
- Date: June 15, 2026
- Legal basis: Section 47(2) of the CGST Act, 2017
- Benefit: Full waiver of late fees for delayed GSTR-3B filings
- Deadline to avail: July 31, 2026
- Who benefits: MSMEs meeting the eligibility criteria (see next section)
In plain English: if your MSME client (or family business) has pending GSTR-3B filings, and they file everything before July 31, 2026, the late fee is waived. After that date, normal Section 47(2) penalties resume.
MSME Eligibility: Who Qualifies for the Waiver?
Not every GST registrant automatically gets this waiver. Based on the notification's MSME scope, here is a checklist of who typically qualifies under such amnesty schemes. Verify specific turnover thresholds on the official portal before filing.
| Criterion | Typical Requirement |
|---|---|
| Registration type | Regular CGST/SGST registrant |
| Business category | MSME (Micro, Small, or Medium Enterprise) |
| Returns in question | GSTR-3B for past periods (specific tax periods as notified) |
| Filing window | Must file on or before July 31, 2026 |
| Tax dues | Outstanding tax must be paid in full — waiver covers fee only, not tax |
| Composition dealers | Generally excluded (they file CMP-08, not GSTR-3B) |
Key point for your exam answers: A late fee waiver under Section 47 does not waive interest under Section 50 of the CGST Act. If tax was due and unpaid, interest at 18% per annum continues to apply from the original due date. This distinction is a favourite MCQ trap.
Step-by-Step: How to File GSTR-3B Under the Waiver
These steps assume you are filing on the GST portal (gst.gov.in) on behalf of an MSME registrant. Walk through this carefully.
Step 1 — Log in to the GST Portal Go to gst.gov.in. Enter the GSTIN (15-digit GST Identification Number) and password. Complete OTP verification.
Step 2 — Check Pending Returns Navigate to: Returns Dashboard → Select Financial Year → Select Tax Period. You will see a list of all pending GSTR-3B filings. Note which months are overdue.
Step 3 — Prepare the Return Data For each pending period, gather:
- Total outward taxable supplies (B2B + B2C)
- Total ITC available (from GSTR-2B auto-populated data)
- Tax payable (CGST, SGST, IGST, Cess separately)
Mini example:
Ravi Traders (MSME, Mumbai) missed GSTR-3B for March 2026.
- Taxable turnover: ₹8,00,000
- GST rate: 18% → Tax = ₹1,44,000 (₹72,000 CGST + ₹72,000 SGST)
- ITC available: ₹30,000
- Net tax payable: ₹1,14,000
- Normal late fee (say 60 days late): 60 × ₹50 = ₹3,000 → waived under Notification 24/2026
Step 4 — Pay Outstanding Tax First Before submitting, pay the net tax liability via the Electronic Cash Ledger. Use Services → Payments → Create Challan. Without paying the tax, the return cannot be filed and the waiver cannot be availed.
Step 5 — File the Return Go back to the Returns Dashboard, open GSTR-3B for the relevant period, fill in the tiles (3.1 for outward supplies, 4 for ITC), verify figures, and click Submit, then File with DSC or EVC.
Step 6 — Verify Late Fee Computation After filing, the system should reflect ₹0 late fee if the notification has been implemented in the portal. If a fee still appears, raise a grievance ticket via gst.gov.in/help/grievance or contact your GST Suvidha Kendra.
Step 7 — Repeat for All Pending Periods File each overdue return one at a time, oldest period first. Do not skip periods — the system generally requires sequential filing.
Section 47(2) Explained Simply — For Your Exam
Section 47 of the CGST Act deals with late fees for delayed filing of returns. Here is how to remember it for exams:
- Section 47(1) → Late fee for GSTR-1 and GSTR-3 (not relevant here)
- Section 47(2) → Late fee for GSTR-3B
- ₹50/day where tax is payable
- ₹20/day for nil returns
- Maximum ₹10,000 per return (as per the current cap, subject to notification)
The government uses its powers under Section 128 of the CGST Act to waive or reduce these fees through notifications. Notification 24/2026 is an exercise of this Section 128 power — that connection is often tested in B.Com and CA Inter theory questions.
Exam tip: If a question asks "Under which section can the government waive GST late fees?" — the answer is Section 128, CGST Act, 2017, not Section 47 (which imposes the fee).
Common Mistakes to Avoid Before July 31
Students assisting businesses often make these errors. Avoid them.
- Paying only the late fee and not the tax — The portal will not accept the return. Tax must be paid first.
- Confusing CBDT with CBIC — Income Tax notifications come from CBDT. GST notifications come from CBIC. Notification 24/2026 is a CBIC notification. Mixing these up costs marks in exams.
- Ignoring interest under Section 50 — The waiver covers fees, not the 18% annual interest on delayed tax payment. Budget for both.
- Filing in the wrong order — Always file older periods first. Filing April 2026 before March 2026 creates system errors.
- Waiting until July 30 — Portal traffic spikes on deadline days. File by July 25 to avoid technical failures.
If you want to test how well you understand GST filing concepts before your next exam, work through a few practice scenarios at SuperAccountant's free quiz — it's structured around real exam-level questions, not just definitions.
Quick Reference Checklist for Filing Under Notification 24/2026
Use this before you sit down at the portal:
- Confirm business is an MSME as per MSME Development Act definition
- Confirm GSTIN is active and not suspended
- Download GSTR-2B for all pending periods to verify ITC
- Calculate net tax for each pending period
- Create and pay challan for all outstanding tax + interest (Section 50)
- File GSTR-3B returns, oldest period first
- Screenshot confirmation of ₹0 late fee on each return
- Complete all filings before July 31, 2026
- Check the official CBIC portal (cbic-gst.gov.in) for any amendments to the notification
What This Means for Your Studies
If you are a B.Com third-year student or a CA Inter candidate, this notification is not just practical news — it is live exam material. Questions on amnesty schemes, waiver powers under Section 128, and GSTR-3B computation are standard in university papers and ICAI mock exams.
More importantly, helping a real business avail this waiver correctly — working through the portal, computing interest, checking GSTR-2B — is exactly the kind of practical exposure that differentiates candidates in placement interviews. If you are building towards your first accounting role, check out the SuperAccountant cohort programme, which covers hands-on GST filing alongside the theory.
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.