As per Notification No 64/2017 – Central Tax, the late fee for per day for filing of GSTR – 3B is Rs 25 in case of return where the taxpayer has to pay tax and Rs 10 per day in cases where the taxpayer has to file Nil return.
As per Notification No. 50/2017 – Central Tax dated 24th Oct 2017, the late for the month of August and September has been waived off for all the taxpayers who have not filed GSTR – 3B by the due date.
Late fee waived for delayed filing of GSTR – 3B for the month of July 2017 http://india-gst.in/wp-content/uploads/2017/09/notfctn-28-central-tax-english.pdf
Section 6.1 of GSTR – 3B, details of payment for GST has to be shown. Amount of Tax Payable, Amount of Tax paid under GST utilizing the ITC and balance amount in cash has to be shown along with interest and late if any payable for CGST, SGST, UTGST, IGST and Cess.
As per the CGST Act, The time of supply for interest, late fee or penalty for delayed payment of any consideration is the date on which the payment is received by the supplier but not on the date on which the suppliers raises the debit note.
The concerned officer who is approving the refund order may deduct the amount which is due to be paid to the applicant, if there are any amounts pending to the GST authorities in form of penalty or interest or late fee or any tax due and pay the balance amount if any remaining. The amount will be deducted only the same is not stayed by any court or tribunal.
Part B of the GSTR – 3 will be auto-populated for Tax, Interest, late fee, penalty from Cash Ledger and Input Tax Credit Ledger in GSTR – 3.