GST Late Fee and Interest for Late GSTR-3B: How It Is Calculated

When GSTR-3B is filed after its due date, the GST portal charges two separate things: a late fee, which is a per-day charge for the delay in filing, and interest, which is charged on the tax that was paid late. The portal's user guide states the late fee as Rs 25 per day with liability or Rs 10 per day for nil liability, under CGST and SGST each, and interest is computed under Section 50 of the CGST Act. This article explains how each piece works and how to estimate them before you file.

Who this is for and what you will have

This is for business owners, accountants and GST practitioners in India who have missed a GSTR-3B due date and want to understand what the portal will show. By the end you will know which numbers are fixed by the portal's documented rules, how the interest base differs between the current and earlier periods, and how to work out an estimate. The figures below come from the GST portal's own help and the CBIC text of the Act. Rates and caps are changed by notification, so confirm the amounts shown on the portal for your return before paying. Information was checked in October 2026.

Late fee and interest are different charges

The portal's guide says the late fee is computed as [date of filing minus due date] multiplied by Rs 25 per day (in case of any liability) or Rs 10 per day (in case of nil liability), per Act, meaning each of CGST and SGST. Because the figure applies under each Act, the combined daily amount is double. The guide also says there is no late fee payable for IGST and cess, and that negative liability is treated as nil liability for late fee calculation.

Interest is computed by a formula the guide describes as [date of filing minus due date] multiplied by the applicable interest rate, applied to the relevant amount of tax.

What the Act says about the interest rate

Section 50 of the CGST Act sets the framework. The rate for late payment is fixed by the Government on the recommendation of the GST Council and cannot exceed eighteen per cent a year. A higher ceiling of twenty-four per cent applies to input tax credit that was wrongly availed and utilised, and the interest on that runs from the date of utilisation until the credit is reversed or tax is paid. The actual rates are fixed by notification, so use the figure shown by the portal's interest calculation as the authority. For estimates, many practitioners use the eighteen per cent ceiling, and the example later in this article does so only as a labelled assumption.

Which amount does interest apply to

This is where many estimates go wrong. The portal says interest is computed in accordance with the first proviso to Section 50, as amended, and:

• For liability in the current period, interest applies only to the portion paid by debiting the electronic cash ledger. This is the net liability, because the part paid with input tax credit is not charged.
• For liability from previous periods, interest applies to the entire liability, the gross amount.

If a liability relates to an earlier tax period, you must provide the period-wise breakup using the Tax Liability Breakup button so the system can compute interest correctly. The portal requires this even when the return is filed on time. Interest in Table 5.1 is auto-populated from the liability breakup given in the previous return period, and the Re-compute Interest button recalculates it with the latest parameters. The portal notes there is no limit on how many times you can use it.

Interest is not calculated on negative liability. If the previous period shows positive liability, interest applies only to that portion.

Step by step: estimate the cost of a late return

1. Find the due date and the filing date. Count the days after the due date until the date you will file. The portal's formula uses the filing date and the due date.
2. Separate CGST, SGST, IGST and cess. Late fee applies under CGST and SGST only.
3. Decide if there is liability. If the return has tax liability, use Rs 25 per day for each of CGST and SGST. If the liability is nil, use Rs 10 per day for each. Negative liability counts as nil for the late fee.
4. Check for a cap. Late fee is subject to maximum limits that have been set by notification and vary by circumstance. Take the figure the portal computes and do not assume a number from memory.
5. Work out the interest base. For the current period, use the tax paid through the cash ledger. For earlier periods, use the full liability.
6. Apply the rate and the days.

Worked example

This example is illustrative, uses invented numbers and assumes an interest rate of 18 percent a year, which is the statutory ceiling. Confirm the rate on the portal.

Suppose a business has a current-period liability of Rs 100,000 in total, of which Rs 60,000 is paid with input tax credit and Rs 40,000 is paid in cash. Return is filed 10 days late.

Late fee (with liability):
  CGST: 10 days x Rs 25 = Rs 250
  SGST: 10 days x Rs 25 = Rs 250
  Total before any cap  = Rs 500
 
Interest (current period, net liability paid in cash):
  Rs 40,000 x 18% x 10 / 365 = about Rs 197.26

The late fee and interest are both payable, and they are paid separately through the electronic cash ledger. Interest runs on the tax that was late, not on the late fee. If the same business had instead left an earlier period's tax unpaid, interest would be charged on the whole earlier-period liability, not only on a cash portion.

Where the portal shows the numbers

In the GSTR-3B return, Table 5.1 shows interest and late fee. The portal says both are auto calculated by the system based on the date of filing and the due date. When you prepare the return, check the interest and late fee entries before you make payment, and use Re-compute Interest if the parameters have changed. If you file the return in the quarterly scheme, the QRMP advisory on the portal says late fee applies to delayed filing there too.

Troubleshooting

• Nil return option is disabled. A nil GSTR-3B cannot be filed if there is outstanding interest or late fee, including system-calculated interest for the current period. Pay the dues, or prepare the return in the normal way.
• Interest looks too high. You may have an earlier-period liability without a period-wise breakup. Use the Tax Liability Breakup button and provide the correct tax periods, then re-compute.
• Interest only is shown. If interest is due from a previous period but GSTR-1 has not been filed or GSTR-2B generated for the current month, the system-generated PDF may show only interest values.
• Late fee shown on IGST. The portal says there is no late fee payable on IGST and cess; if you see one, recheck the entries before paying.
• Figures differ from an online calculator. Calculators often use fixed assumptions on rates and caps that may not match current notifications. Treat the portal's computation as authoritative.

Checklist

• Note the due date for your filing frequency and the date you plan to file.
• Confirm whether the return has liability or is nil.
• Provide the tax liability breakup for any earlier-period liability.
• Review Table 5.1 for interest and late fee before paying.
• Pay late fee and interest from the electronic cash ledger and keep the challan.
• Record the reason for the delay and set a reminder so that the next due date is not missed.

For the return itself, see /blog/gstr-1-vs-gstr-3b-differences, and for how credit matching affects what you pay, see /blog/gst-input-tax-credit-rules-itc-3b-2b-matching.

References

• GST portal user guide: Form GSTR-3B FAQs
• GST portal: How can I create, save, pay taxes and file Form GSTR-3B
• CBIC: CGST Act 2017, Section 50 (interest on delayed payment of tax)
• CBIC: CGST Act 2017, Section 47 (levy of late fee)
• GST portal: Advisory on Quarterly Return with Monthly Payment scheme