Missed GSTR-3B? You pay two separate things: a late fee for the delay in filing, and interest for the delay in paying tax. Here's how each works.
1. Late fee
| Type | Per day (CGST + SGST) | Maximum |
|---|---|---|
| Nil return | ₹20 (₹10 + ₹10) | ₹500 |
| Turnover up to ₹1.5 crore | ₹50 (₹25 + ₹25) | ₹2,000 |
| Turnover ₹1.5 - 5 crore | ₹50 | ₹5,000 |
| Turnover above ₹5 crore | ₹50 | ₹10,000 |
For an inter-state (IGST) only return, the fee is charged as IGST at the same total. The late fee is paid in cash - it can't be paid from your ITC.
GSTR-1 has the same late fee structure. GSTR-9 has its own: ₹50/day (turnover up to ₹5 crore) or ₹100/day (₹5-20 crore), capped at 0.04% of turnover, and ₹200/day capped at 0.5% above ₹20 crore.
2. Interest
18% a year on the tax paid late, for the days from the due date to the date of payment. Section 50 (as amended in 2021, with effect from 1 July 2017) charges interest on the net cash liability - the tax you pay in cash after using ITC - not the gross tax, for returns filed late.
Interest = tax paid in cash × 18% × days late ÷ 365
Worked examples
Example 1 - small trader, 12 days late. Turnover ₹80 lakh, tax payable in cash ₹42,000, filed 12 days late.
- Late fee: 12 × ₹50 = ₹600 (below the ₹2,000 cap)
- Interest: 42,000 × 18% × 12 ÷ 365 = ₹249
- Total: ₹849
Example 2 - nil return, 40 days late. 40 × ₹20 = ₹800, capped at ₹500. No interest (no tax).
Example 3 - QRMP, ₹38,000 tax, 15 days late, turnover ₹3 crore.
- Late fee: 15 × ₹50 = ₹750 (cap ₹5,000)
- Interest: 38,000 × 18% × 15 ÷ 365 = ₹281
Use the free late fee calculator for your numbers.
How to file a late GSTR-3B
- Log in to the GST portal → Returns Dashboard → choose the period.
- Check Table 3 (auto-filled from GSTR-1/1A - fix mistakes via GSTR-1A first).
- Fill ITC in Table 4 (auto-drafted from GSTR-2B; check it).
- The portal computes the late fee and interest automatically in Table 5.1 / 6.1.
- Create a challan for the cash amount, pay, then offset liability and file with DSC or EVC.
Don't wait too long
- From the next period, you can't file GSTR-3B until the earlier one is filed.
- Your buyers' ITC depends on your GSTR-1; repeated delays hurt business relationships.
- Non-filing for two months (monthly) or two quarters (QRMP) can block your e-way bills, and long non-filing can lead to cancellation of registration.
- Returns can't be filed at all after three years from the due date.