E-Invoice and E-Way Bill Mismatch: GST Notice Reply

A GST notice has arrived comparing your e-invoices, e-way bills, GSTR-1 and vehicle movement data, and the numbers do not agree. An e-way bill mismatch GST notice is usually not an allegation of evasion on its face. It is an exception report: the department's analytics found an invoice without a matching movement document, or a movement document for goods your return does not show. This article explains how that comparison is built, how to reconcile the four data sets, and how to draft a reply that answers the officer's actual question.

Why the department compares invoice and movement data

Under section 68 of the CGST Act, 2017, an officer in charge of a conveyance can intercept goods in movement and require the person in charge to produce the documents listed in rule 138A of the CGST Rules, 2017: the tax invoice or bill of supply, the e-way bill and, where relevant, a delivery challan. The same section allows inspection of the goods and detention where the officer has reason to believe they are being moved in contravention of the Act.

Movement data sits on three separate systems. GSTR-1 carries invoice-level supplies. The Invoice Registration Portal carries every IRN generated under rule 48(4), with the buyer's GSTIN, invoice number, date and value. The e-way bill system carries EWB-01, which includes the invoice number as keyed in by the consignor or transporter, the HSN, the value, the vehicle number in Part B and the validity period. CBIC's Directorate General of Analytics and Risk Management runs the cross-matching and routes exception cases to field formations.

The first document you usually receive is not a demand. It is a scrutiny notice under section 61 of the CGST Act, issued in Form GST ASMT-10 under rule 99 of the CGST Rules, asking you to explain the discrepancy within 30 days. Your reply goes in Form GST ASMT-11. If the officer is not satisfied, the matter can later move to section 73 or section 74.

Reconciling IRN, e-way bill and GSTR-1 line by line

The four identifiers that must agree

Every B2B consignment above ₹50,000 has at least three identifiers and sometimes four. The invoice number and date, exactly as printed on the tax invoice. The IRN, a 64-character hash tied to that invoice number. The e-way bill number, generated either through the Invoice Registration Portal, where Part A is auto-populated from the invoice, or manually on the e-way bill portal, where someone types the invoice number by hand. And the GSTR-1 line, which must carry the same invoice number, date and taxable value that the IRN carries.

The matching key is your GSTIN plus the invoice number. A single character typed differently in the e-way bill, whether an extra zero or a slash replaced by a hyphen, breaks the match and produces an exception even though the goods and the tax are entirely genuine.

Where the mismatches actually come from

• Manual e-way bill entry. By a wide margin the most common cause. Invoice typed as SVP/25-26/1208 when the invoice is SVP/25-26/1203.

• Timing across months. Invoice dated 31 March, e-way bill generated 1 April, GSTR-1 filed in the next tax period.

• Wrong document type. A B2C invoice reported in the B2B table, or a bill of supply or delivery challan treated as a tax invoice.

• Consignment value. Several invoices for one consignment clubbed into a single e-way bill, so the per-invoice match fails.

• Expired validity without extension. The vehicle broke down, the trip ran longer, and the e-way bill lapsed before delivery.

Explaining cancelled, amended and return trips

Rule 138(9) allows an e-way bill to be cancelled electronically within 24 hours of generation where goods are not transported, or are not transported as per the details furnished. A cancelled e-way bill stays visible in the system with its status marked as cancelled. If the notice counts it as a live movement, say so, and attach the cancellation acknowledgement with its date and time. Cancellation beyond 24 hours is not permitted, so where a trip falls through late you must bring the goods back under a fresh document instead of leaving a live e-way bill hanging.

Rule 138(10) fixes validity at one day for a distance up to 200 km and one additional day for every 200 km or part thereof, extendable only within eight hours of expiry. Where goods are transhipped mid-route, Part B has to be updated with the new conveyance and the transhipment details. An unamended Part B is the reason many vehicle-mismatch flags arise.

Return trips need their own paper trail. Where goods come back because the buyer rejected them, the original invoice stands and a credit note under section 34 records the reduction, with the return movement covered either by a fresh e-way bill against the credit note or, where no supply is involved, by a delivery challan under rule 55. Job work returns, reversed stock transfers and goods sent for repair all fall in this bucket. Each needs a document the officer can tick against the original invoice.

Worked scenario: a Coimbatore pump maker and a November notice

Sri Venkateswara Pumps Pvt Ltd, a Coimbatore manufacturer, files GSTR-1 for November 2025 showing 212 B2B invoices. In February 2026 it receives Form GST ASMT-10 for that month flagging three items.

First, invoice SVP/25-26/1187 dated 14 November 2025: taxable value ₹6,50,000, IGST at 18% of ₹1,17,000, total ₹7,67,000, consigned to a dealer in Nagpur. The e-way bill was generated on 14 November for a distance of 1,240 km, valid for seven days until 20 November. The truck broke down near Hyderabad on 17 November. Goods were transhipped on 19 November into a second truck and Part B was updated the same day, but delivery happened on 22 November, two days after expiry.

Second, invoice SVP/25-26/1191 dated 15 November, ₹1,84,000, reported in GSTR-1 with an e-way bill cancelled the same afternoon because the dealer's credit hold had not cleared. The goods never left the factory. Credit note CN/25-26/044 was issued on 20 November and reported in the December return.

Third, invoice SVP/25-26/1203 dated 28 November, ₹2,15,000, where the e-way bill generated on 29 November quoted the invoice number as SVP/25-26/1208.

The reply disputes none of these facts. It sets them out in a table, attaches the transporter's lorry receipt and breakdown intimation for the first, the cancellation acknowledgement and credit note for the second, and a declaration with the corrected e-way bill for the third, and asks the officer to close the scrutiny. Exposure on the first item alone, if section 129 were invoked, would be a penalty equal to 200% of the tax on the goods, that is ₹2,34,000.

Structuring the reply to an e-way bill mismatch GST notice

Keep the reply short and let the annexure do the work. Open with the notice reference, the period and the number of line items flagged. State, item by item, what happened and which document proves it. Close with a reconciliation statement and a list of enclosures.

The table should carry one row per flagged invoice, with these columns: invoice number and date, IRN, e-way bill number and date, validity end date, GSTR-1 period and taxable value, explanation code, annexure reference. Use plain codes such as C for cancelled, T for transhipment or extension, E for keying error corrected, R for return with credit note and M for month-end timing. An officer reading thirty rows wants to see that each one has a code and a document behind it.

Under section 155 of the CGST Act the burden of proving a claim lies on the person making it, so assertions without documents will not move the file. File the reply on the portal as ASMT-11 within the 30 days allowed. A covering letter handed over at the counter is not a reply.

Penalty exposure and preventive controls

Two provisions matter. Section 129 deals with goods detained or seized in transit and carries a penalty equal to 200% of the tax payable on the goods. Section 122 covers supplying goods without an invoice or with an incorrect invoice, with a penalty of ₹10,000 or the tax sought to be evaded, whichever is higher. In most genuine mismatch cases the correct outcome is closure at the scrutiny stage; the risk is that a thin reply pushes the officer towards section 129 or section 130.

Documents to keep for every consignment

Tax invoice, e-way bill with the Part B history, transporter's lorry receipt or bilty, weighment slip where relevant, proof of delivery with date and signature, and any transhipment or extension record. For cancelled trips, the cancellation acknowledgement with its timestamp. For returns, the credit note and the return e-way bill or delivery challan. Store these against the invoice number, not against the date, so that a query two years later can be answered in an hour.

Common mistakes in the reply

Arguing that the notice is invalid before explaining the transactions. Attaching all 212 invoices instead of the three that were flagged. Explaining the e-way bill but ignoring the GSTR-1 entry. And leaving the reply to the last week, which removes any chance of getting the transporter's records in time.

• Download the ASMT-10 annexure and list every flagged invoice number before opening any other file.

• Pull the IRN, e-way bill and GSTR-1 record for each flagged invoice into one working sheet.

• Match on GSTIN plus invoice number, never on value alone.

• Obtain the transporter's lorry receipt, transhipment note and breakdown intimation in writing.

• Attach cancellation acknowledgements and credit notes for trips that never happened.

• File Form GST ASMT-11 on the portal well inside the 30-day window, with a signed reconciliation table.

• Fix the root cause, manual invoice keying, by generating e-way bills from the IRN wherever possible.

If a notice is already on your desk, the single most useful thing you can do this week is build the reconciliation sheet for the flagged invoices and get the transporter's documents in writing; everything else in the reply follows from that sheet.

This article is for general information only and is not legal advice. Consult a qualified professional for your specific facts.