Why Amazon and Flipkart rejected your GST invoice

Marketplace invoice validation is automated, and the feedback you get is usually a status flag rather than an explanation. The invoice is marked non-compliant, the payout moves to hold, and you are left comparing documents line by line to work out which field did it.

The checks themselves are not mysterious. They are the statutory invoice requirements under Rule 46 of the CGST Rules plus arithmetic verification. Below are the ones that fail most often, in roughly the order we see them.

1. Wrong tax head — IGST charged instead of CGST + SGST

The most common failure by a wide margin, and the most expensive, because the total tax often looks correct. The trigger is usually a buyer whose GSTIN belongs to one state while delivery goes to a warehouse in another. Place of supply decides this, not the billing address — the place of supply guide works through the cases.

2. Invalid or inactive GSTIN

A GSTIN is 15 characters with a fixed structure: two-digit state code, ten-character PAN, one entity code, the letter Z, and a checksum character. A transposed digit still looks plausible to a human and fails the checksum instantly.

Format is only half of it. A GSTIN that was valid when you onboarded the buyer may since have been cancelled or suspended, and an invoice against a cancelled registration is not going to survive validation — or give your buyer usable credit.

3. Missing, short, or wrong HSN / SAC code

HSN reporting requirements scale with turnover, and the number of digits matters: businesses above the prescribed threshold must report six digits, smaller ones four. Reporting a four-digit code where six are required is a rejection, even though the code itself is correct as far as it goes.

The subtler version is an HSN code that is valid but does not carry the rate you applied. The code and the rate have to agree with each other.

4. Tax arithmetic that does not reconcile

Taxable value multiplied by rate must equal the tax charged, per line, and the line totals must sum to the invoice total. Rounding applied per line and again at the bottom introduces a rupee or two of drift, and an automated check does not care that the difference is small.

5. A missing mandatory field

Rule 46 lists what a tax invoice must contain. The ones most often left off: place of supply on inter-state supplies, the recipient's state and state code, the HSN summary, and a declaration where the invoice is signed digitally. An invoice missing any of them is not a valid tax invoice regardless of how correct the tax is.

6. Invoice numbering breaks the rules

Invoice numbers must be consecutive, unique within the financial year, and no longer than 16 characters. Series that restart mid-year, duplicate across sales channels, or carry characters outside letters, digits, hyphen and slash all cause problems — and duplicates in particular tend to surface later as a GSTR-1 upload failure rather than at invoice time.

7. Invoice date outside the acceptable window

An invoice dated after the shipment, dated in a return period you have already filed, or backdated into a closed period will be flagged. Time-of-supply rules fix when the invoice must be raised — for goods, on or before removal or delivery.

8. Reverse charge flagged incorrectly

The reverse charge field is a yes or no that changes who pays. Marking a normal supply as reverse charge means you have charged tax on a document that says the recipient owes it, which is contradictory on its face. The reverse mistake — a genuine RCM supply not flagged — leaves the tax unpaid by anyone.

9. Missing IRN or QR code where e-invoicing applies

If your aggregate turnover crosses the e-invoicing threshold, a B2B invoice without an Invoice Reference Number and signed QR code from the IRP is not a valid invoice at all, and your buyer cannot claim credit against it. The threshold has been lowered repeatedly, so a business that was outside the net last year may be inside it now without having noticed.

If a payment is already on hold

• Fix the invoice at source rather than editing the PDF — the version that has to be correct is the one that reaches GSTR-1.
• If the original was already reported, correct it with a credit note or an amendment in the next GSTR-1 rather than silently reissuing the same number.
• Check whether the same defect affects the rest of the batch. Wrong tax heads and short HSN codes are configuration problems, so they are rarely isolated.
• Re-validate before resubmitting, so you are not spending another cycle finding out about the second error after fixing the first.

The invoice checker runs all of the above in one pass and tells you which line failed and why.