When an E-Invoice Is Missed or Wrong

An e-invoicing error usually surfaces late. A truck is stopped and the officer finds a printed invoice with no QR code. A customer’s GSTR-2B shows a credit note that was never meant to be issued. An IRN carries the wrong GSTIN and the 24 hours to cancel it have passed. The supplier may have paid the tax in full, but the paperwork does not match what the rules require.

This guide covers what follows a missed or wrong e-invoice. It explains the effect of rule 48(5), the recipient’s credit and the penalty provisions. It then sets out how errors are corrected, and how the courts have dealt with goods stopped in transit without an e-invoice. Who must e-invoice is in guide 701, and how an IRN is generated and cancelled is in guide 702.

The rule: not an invoice at all

Rule 48(5) reads:

Every invoice issued by a person to whom sub-rule (4) applies in any manner other than the manner specified in the said sub-rule shall not be treated as an invoice.

The rule does not impose a penalty. It takes away the document’s status as an invoice. That matters in three places:

• The supplier. Section 31 requires a tax invoice for every taxable supply. A document that “shall not be treated as an invoice” leaves the supply without one.
• The recipient. Its credit depends on holding a tax invoice.
• The goods in transit. Rule 138A(1)(a) requires the person in charge of a conveyance to carry “the invoice or bill of supply or delivery challan”.

The tax is a separate matter. The supply has still taken place, the time of supply is still fixed by the Act, and the tax is still payable. Rule 48(5) changes the document, not the liability.

The supplier’s exposure to penalty

The Act has no penalty written for e-invoicing in particular. Two general provisions are relevant.

Section 122(1)(i). Section 122(1) penalises a taxable person who “supplies any goods or services or both without issue of any invoice or issues an incorrect or false invoice with regard to any such supply”. The penalty is “ten thousand rupees or an amount equivalent to the tax evaded … whichever is higher”. Where the tax has been reported and paid, the tax evaded may be nil. In that case the Rs 10,000 floor is the operative figure.

Section 125. Section 125 is the general penalty, up to Rs 25,000, for a contravention “for which no penalty is separately provided for”. The Government has treated section 125 as the provision for breaches of the companion rule on dynamic QR codes. Notification No. 28/2021-Central Tax waived “the amount of penalty payable … under section 125” for not complying with Notification No. 14/2020 between 1 December 2020 and 30 September 2021. No similar waiver exists for e-invoicing.

Which provision applies in a given case is for the officer to state. Section 126 governs every penalty. Under it:

• No penalty may be imposed for “minor breaches of tax regulations or procedural requirements”. A breach is minor where the tax involved is less than Rs 5,000. An omission in documentation is covered where it is “easily rectifiable” and made “without fraudulent intent or gross negligence”.
• The penalty must be “commensurate with the degree and severity of the breach”.
• No penalty may be imposed without an opportunity of being heard.
• The order must “specify the nature of the breach and the applicable law”.

The recipient’s credit

Section 16(2) allows credit only if, among other conditions:

• (a) the recipient “is in possession of a tax invoice or debit note issued by a supplier registered under this Act”
• (aa) “the details of the invoice or debit note referred to in clause (a) has been furnished by the supplier in the statement of outward supplies and such details have been communicated to the recipient”

The two clauses can come apart. A supplier who did not e-invoice may still report the invoice in GSTR-1 by hand. It then reaches the recipient’s GSTR-2B, and clause (aa) is met. But clause (a) refers to a “tax invoice”, and rule 48(5) says the document “shall not be treated as an invoice”. The department can therefore question the credit under clause (a) even where the supply, the payment and the GSTR-2B entry are all in order. The conditions themselves are explained in the guide on section 16.

The point has been raised but not decided. In Global One Resources LLP v Deputy Commissioner, SGST (Rajasthan High Court, 17 January 2023), show cause notices proposed, among other things, to deny the petitioner credit on invoices from one supplier. The ground was that the supplier had not issued e-invoices under rule 48. The petitioner replied that the supplier was not required to e-invoice in that year, because its turnover crossed the limit only in 2021-22. The Division Bench held that the supplier’s turnover and obligation were questions of fact. It declined to interfere at the notice stage, leaving “all the issues raised” to the adjudicating authority. The case shows the department taking the point. It is not a ruling that rule 48(5) defeats credit.

A recipient can check whether a document was registered on an IRP. The verification app and the “verify signed invoice” facility on the e-invoice portal read the signed QR code or JSON.

Correcting an e-invoice that is wrong

The IRP allows no edits. What can be done depends on time.

Within 24 hours. The supplier cancels the whole IRN, after first cancelling any e-way bill generated on it. It then issues a fresh document under a new number, because the cancelled number cannot be reused. The e-invoice portal’s FAQs describe this as the “only option” for a document with an error. Partial cancellation is not possible.

After 24 hours. The IRN stands. GSTN’s overview of the system says amendment of an e-invoice is done “only on GST portal, while filing GSTR-1”. There are three routes, each under its own provision:

• Before GSTR-1 is filed. The auto-populated record can be edited in GSTR-1. The portal’s FAQs say that once a record is changed, “the Source, IRN, and IRN Date fields will become blank”. Draft records can also be deleted until the return is filed. The procedure is in the guide on filing GSTR-1.
• After GSTR-1 is filed. The record is amended in GSTR-1A for the same period, or through the amendment tables of a later GSTR-1. Section 37(3) sets an outer limit for rectification: 30 November after the end of the financial year, or the date of the annual return if earlier. The detail is in correcting mistakes in returns.
• A credit or debit note under section 34. Where the value or tax was overstated, or goods were returned, a credit note is issued. Where it was understated, a debit note is issued. A supplier required to e-invoice must register these notes on an IRP too, as they are among the three covered document types. A credit note must be declared by 30 November following the end of the financial year of the supply, or the annual return if earlier. Under the proviso to section 34(2), the supplier’s tax is not reduced unless a registered recipient has reversed the credit.

A GSTR-1 amendment changes the return, not the IRN. The signed record on the IRP still shows the original data. Where the error is the recipient’s GSTIN, the wrong recipient sees the document in its Invoice Management System and can reject it there.

A document that should not have been reported. This covers a duplicate, a B2C sale reported as B2B, or a document for a supply that did not take place. Within 24 hours it is cancelled. After that, it is removed from the draft GSTR-1 before filing, or reversed through the amendment or credit note routes above. Which route fits depends on whether the document reflected a supply at all.

An e-invoice not generated, or generated late

Turnover of Rs 10 crore and above. From 1 April 2025 the IRPs reject a document more than 30 days old (GSTN advisory of 5 November 2024). A document that missed the window cannot be e-invoiced at all, and remains outside rule 48(4).

Below Rs 10 crore. No portal limit applies, and the e-invoice portal’s FAQs say a missed invoice “may still” be registered later.

Rule 48 does not say whether registering an invoice late cures rule 48(5). The cases below show courts treating a later IRN as evidence that tax was not being evaded. None of them holds that the later IRN makes the original document an invoice.

Goods stopped without an e-invoice: the cases

When goods move under a manual invoice and an e-way bill but no IRN, officers have detained them under section 129 and proposed penalty at 200 per cent of the tax. The detention procedure itself is covered in guide 707. The High Courts have not taken one line.

Nancy Trading Company v State of U.P. (Allahabad High Court, 15 July 2024). The goods moved with a tax invoice, transport receipts and an e-way bill, but no e-invoice. The petitioner said it had not realised that the threshold had fallen from Rs 20 crore to Rs 10 crore. The court noted that all documents required by rule 138A were carried and that there was no discrepancy in quantity or quality. It called the failure a “human error” and a “bona fide mistake”. It held that “in absence of any finding with regard to mens rea the proceeding under section 129(3) of the Act cannot be initiated”, and quashed the penalty and the appellate order.

Osel Devices Ltd v Assistant Enforcement Officer (Kerala High Court, 7 November 2024). The goods were detained on 12 May 2023 for want of an e-invoice, which the petitioner generated the same day. A penalty of Rs 12,12,120 was imposed under section 129. The court followed its earlier decision in T.P. Metal Roofings, as extracted in this judgment. That decision held that section 129 penalty is not authorised “in cases where only minor discrepancies are noticed”. It is reserved for violations that may lead to evasion, an intent to evade, or repeated violations. The court quashed the order and left the officer free to impose penalty under section 122, “keeping in mind” section 126.

Kramski Stamping and Molding India Pvt Ltd v State Tax Officer (Madras High Court, 13 February 2023) went the other way on its facts. The supplier said a software glitch had prevented an e-invoice for a scrap sale. The officer found that the printed e-invoice produced was “a manipulated one” and imposed penalty of Rs 47,79,721. The court did not interfere, because reasons had been given after a reply. It directed the petitioner to the statutory appeal, with provisional release on furnishing security.

M/s Aqua Excel v State Tax Officer (Madras High Court, Madurai Bench, 3 October 2024) involved an export consignment. It was detained on 7 August 2024 for want of an e-invoice, which the exporter generated the next day. The court distinguished Kramski, where bona fides were absent, and found the case “closer to” Nancy Trading. It did not quash the penalty. Instead it directed provisional release if the exporter showed the transaction in its GSTR-1 as a zero-rated supply. It left the penalty to be challenged in appeal under section 107. The judgment is on gst.bharattax.net.

These decisions were given on their facts. Each turned on whether the documents carried matched the goods, whether tax was otherwise accounted for, and whether the record suggested an attempt to evade. No appeal or special leave petition against any of them has been traced, and no Supreme Court ruling on rule 48(5) has been found. Where an order is passed, the appeal route is set out in the appeal ladder.

What can be done, in order

1. If the error is found within 24 hours of the IRN, cancel any e-way bill on it, cancel the whole IRN, and register a corrected document under a new number.
2. If 24 hours have passed but GSTR-1 for the period is unfiled, edit or delete the auto-populated record before filing.
3. If GSTR-1 is filed, amend through GSTR-1A or a later GSTR-1 within the section 37(3) limit. Where the value or tax changes, issue an e-invoiced credit or debit note under section 34, within its own time limit.
4. If an invoice was never e-invoiced, register it on an IRP where the portal still accepts it. For taxpayers at Rs 10 crore and above, that is within 30 days of the document date.
5. If goods are detained or a penalty or credit denial is proposed, reply within the time the notice gives. Any penalty order must name its provision and is subject to section 126 and to appeal.

The next guide in this set, E-Way Bills: When One Is Needed, turns from invoices to the movement of goods.