It is easy to click "reject" on the wrong record in the Invoice Management System (IMS). If you have already filed GSTR-3B for that period, can you still get the input tax credit? Yes. GSTN's FAQ explains the route, which needs your supplier's help.

If you wrongly rejected an invoice, debit note or e-commerce document

  1. Ask the supplier to report the same record, without any change, in either:
    • GSTR-1A for the same return period, or
    • the amendment table of GSTR-1/IFF of a later period, within the time limit.
  2. Accept the re-reported record in IMS and recompute GSTR-2B.
  3. You get ITC for the full value, because the original was rejected.

Note: you can take this ITC only in the GSTR-2B of the tax period in which the record is re-reported.

Does the supplier pay tax twice? No. The amendment table works on the difference in value. Since the record is unchanged, the extra liability is zero.

If you wrongly rejected a credit note

A rejected credit note means you didn't reduce your ITC, but you should have.

  1. Ask the supplier to report the same credit note, unchanged, in GSTR-1A for the same period or in the amendment table of a later GSTR-1/IFF.
  2. Accept it in IMS and recompute GSTR-2B. Your ITC is reduced by the full credit note value.

What happens on the supplier's side? When you rejected the credit note, the supplier's liability was added back in their open GSTR-3B. When they re-report it, their liability reduces again by the same amount. The net effect counts only once.

Tips to avoid this

  • Use "pending" if you are unsure, where that option is allowed, instead of rejecting.
  • Add a remark when rejecting, so the supplier knows why.
  • Check IMS carefully before filing GSTR-3B.

Official source