Credit Notes against cancellation of Invoices issued to SEZ Developer

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Dipesh (Querist)
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26 June 2025 We issued service invoice (June-24) to SEZ unit, now customer is not accepting this invoices. Now we have to cancel this invoices through issuing credit notes ? In this scenario what will be the question arises in GST audit or scrutiny because cancellation transactions are more than expected. May department ask to pay IGST or some penalties in future while doing audit ???

Please elaborate.

Thanks in advance.

Aashok Kumar Sharma

Aashok Kumar Sharma (Expert)
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12 August 2025 GST Treatment for Credit Notes to SEZ Developer:
Credit Note is the Correct Way to Cancel/Adjust Invoice
As per GST law, if an invoice needs to be canceled or value reduced, a credit note must be issued referencing the original invoice.
Impact on Output Tax Liability:
Since supplies to SEZ units are zero-rated supplies (IGST at 0%), no output tax liability arises on the original invoice.
Therefore, issuing credit notes to cancel the invoice does not result in IGST liability, as the original supply was zero-rated.
Refund/ITC Considerations:
If you had claimed input tax credit (ITC) related to this invoice, the credit note reduces your output, and accordingly, the ITC adjustment is affected.
Since IGST was zero, this typically has no tax reversal issue.
Possible GST Audit / Scrutiny Questions:
Why is there a high volume of credit notes?
The department may ask for explanations if credit notes are unusually high compared to normal business activity. You should maintain clear supporting documents showing genuine reasons like order cancellations or disputes.
Verification of genuineness of transactions:
The department may check if invoices and credit notes correspond to actual business transactions, not to evade tax.
Penalties or IGST Demand?
Since supplies to SEZ developer are zero-rated, cancellation through credit notes should not attract IGST or penalties if properly documented and filed.

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