E-Way Bill and E-Invoice System Updates: GSTN Advisory and Compliance Guide

Every GST-registered business in India that transports goods or generates B2B invoices above the applicable threshold is directly affected by the ongoing upgrades GSTN and NIC have made to the e-way bill and e-invoice systems. These are not cosmetic changes. Taken together, they restrict when e-way bills can be generated, how far they can be extended, who must authenticate with multi-factor login, what invoice data the IRP will accept, and which GSTIN must now appear on Bill-To/Ship-To transactions. Non-compliance exposes a business to penalties of Rs. 10,000 or the amount of tax evaded, whichever is higher, along with the risk of vehicle detention and goods seizure during transit.

This guide consolidates the key GSTN advisories on e-way bill and e-invoice system updates issued from December 2024 through mid-2026 and translates each update into specific compliance obligations for finance, accounts, and logistics teams operating in India.

Key GSTN Updates at a Glance

January 2025 Advisory: GSTN Updates to E-Way Bill and E-Invoice Systems

The GSTN issued an advisory in December 2024 notifying that NIC would roll out updated versions of the E-Way Bill and E-Invoice systems effective 1 January 2025. The stated objective was to enhance the security of the portals in line with best practices and government guidelines. Three specific changes were implemented under this advisory, in addition to the phased MFA rollout detailed below.

Multi-Factor Authentication (MFA): Mandatory Rollout by AATO Bracket

Multi-factor authentication requires a portal login using a username, password, and an OTP sent to the mobile number registered with the taxpayer’s GSTIN. The Sandes app is also accepted as an OTP delivery channel. The rollout followed a phased schedule based on aggregate annual turnover:

• Since 20 August 2023: MFA mandatory for taxpayers with AATO exceeding Rs 100 crore
• Since 11 September 2023: MFA optional for taxpayers with AATO exceeding Rs 20 crore
• From 1 January 2025: MFA mandatory for taxpayers with AATO exceeding Rs 20 crore
• From 1 February 2025: MFA mandatory for taxpayers with AATO exceeding Rs 5 crore
• From 1 April 2025: MFA mandatory for all taxpayers and users

As of April 2025, MFA applies universally across all GST portal users, including sub-users and transporters. Businesses must confirm that the registered mobile number is current against their GSTIN, and that sub-users have been created with their individual mobile numbers. Detailed setup instructions are available on the official E-Invoice and E-Way Bill portals.

180-Day Restriction on E-Way Bill Generation from Document Date

Effective 1 January 2025, e-way bills can only be generated for invoices, delivery challans, or other base documents dated within 180 days of the date of e-way bill generation. Documents older than 180 days are ineligible. The same restriction applies to Part-A slips.

In practice: an e-way bill generated on 1 March 2025 cannot be raised against any document dated before 3 September 2024. For businesses with extended inventory cycles, periodic dispatch scheduling, or bulk movement of goods against older purchase orders, this rule requires ERP-level validation at the point of shipment initiation — not as a retrospective check.

360-Day Cap on E-Way Bill Extension from Original Generation Date

E-way bill validity can be extended either up to eight hours before expiry or up to eight hours after, but effective 1 January 2025, total extensions are capped at 360 days from the original date of generation. Once this ceiling is reached, the e-way bill cannot be extended further.

For example, an e-way bill generated on 1 January 2025 can only be extended up to 25 December 2025. Any extension request that would push validity beyond that date is automatically capped at 360 days from generation. If the underlying consignment still needs to move after this point, a fresh e-waybill must be generated which is only possible if the base document falls within the 180-day window.

For consignments that have historically remained under open or extended e-way bills for prolonged periods, this rule closes that option entirely. Compliance and logistics teams need to actively monitor open e-way bills and resolve, close, or reissue them proactively. For the implications this carries during a GST audit by the department, where extended or irregularly managed e-way bills are a common scrutiny area, early resolution significantly reduces exposure.

Further GSTN System Updates: Mid-2025 to 2026

E-Way Bill 2.0 Portal: Dual-Portal Interoperability (Effective 1 July 2025)

GSTN launched the E-Way Bill 2.0 portal (ewaybill2.gst.gov.in) on 1 July 2025, running in parallel with the existing E-Way Bill 1.0 portal (ewaybillgst.gov.in). Both portals are real-time synchronized. E-way bills generated on Portal 1.0 can be updated, extended, or modified on Portal 2.0, and vice versa described by GSTN as “criss-cross” operations. The dual-portal structure eliminates dependency on a single system and maintains business continuity during technical downtime or portal maintenance windows. For a detailed breakdown of the interoperability architecture and its implications for ERP and API integrations, see our insight on GST E-Way Bill 2.0 and interoperable services.

Ship-To GSTIN: Mandatory in E-Way Bill APIs for B2B and SEZ Transactions (Effective 15 June 2026)

GSTN Advisory No. 661 (21 May 2026) introduced a significant structural change in the e-way bill and e-invoice API framework. Effective 15 June 2026, the Ship-To GSTIN is a mandatory field in any IRN and e-way bill API call where ship-to information is present. In B2B and SEZ transactions where the invoicing party differs from the party physically receiving the goods, the GSTIN of the actual delivery location must be declared in the bill not only the billing entity.

This change directly addresses the ITC compliance gap in Bill-To/Ship-To transactions, where goods have historically been diverted in transit without any corresponding GST trail. Businesses with distribution center models, third-party fulfillment arrangements, or multi-location delivery structures are most directly affected. ERP masters, transporter instructions, and API payload templates must be updated to capture and transmit Ship-To GSTIN for every qualifying transaction.

Additionally, as of 15 June 2026, a voluntary e-way bill closure facility has been made permanently available on the production portal, allowing suppliers, recipients, or transporters to formally declare completion of delivery without waiting for natural expiry.

E-Invoice: 30-Day IRP Reporting Window for High-Turnover Businesses

Separately from e-way bill changes, GSTN has tightened the e-invoice reporting window. Businesses above the applicable AATO threshold cannot report invoices to the Invoice Registration Portal (IRP) more than 30 days after the invoice date. An invoice that exceeds this window is rejected by the IRP, receives no IRN, and is invalid for GST and ITC purposes.

This restriction was first introduced for businesses with AATO above Rs 100 crore (effective 1 November 2023) and has since been extended to cover businesses with AATO above Rs 10 crore. Businesses using manual or batch-upload billing processes are most at risk. Real-time IRP integration at the point of invoice generation — not a periodic back-office upload — is now the minimum viable compliance standard for affected entities. Businesses between Rs 5 crore and Rs 10 crore should treat this as an advance signal and review their e-invoice workflows accordingly ahead of any further GST Council extension of the restriction.

Compliance Implications: What Finance and Logistics Teams Need to Address Now

The combined effect of these advisories represents a systematic shift from manual, periodic GST compliance to real-time, system-enforced validation. The compliance burden and the risk from non-compliance has increased materially for businesses across all AATO brackets.

Businesses with AATO above Rs 10 crore face the fullest compliance exposure. MFA is active for all users. The 30-day IRP window applies. All e-way bill generation and extension rules apply. Ship-To GSTIN must be captured and transmitted for qualifying transactions. ERP and API integrations should be validated against both Portal 1.0 and Portal 2.0 environments.

Businesses between Rs 5 crore and Rs 10 crore are subject to mandatory MFA and the full e-way bill rule set. E-invoicing is mandatory. The 30-day IRP window does not currently apply but the direction of travel in GST Council decisions suggests it will be extended. Now is the appropriate time to integrate IRP submission into real-time billing workflows.

Businesses below Rs 5 crore must comply with mandatory MFA across all GST portal users from 1 April 2025. All e-way bill rules apply. E-invoicing is not yet required but the threshold has been reduced progressively since 2020 and further reductions are under active discussion.

Logistics and dispatch teams must treat the 180-day document rule as a hard constraint in shipment scheduling — not a portal error to work around. Document dates must be verified at the point goods are released for movement, not at the point of e-way bill generation. All open e-way bills should be periodically audited against the 360-day extension ceiling to prevent goods being stranded in transit under an expired bill with no renewal option.

How MBG Can Support Your GST Compliance Programme

Understanding the regulatory change is one step. Translating it into process updates across finance, accounts, logistics, and ERP teams while managing the exposure that arises during the transition is another. MBG’s GST advisory and compliance services help businesses assess the impact of GSTN system updates on existing compliance frameworks, identify gaps in e-invoice and e-way bill workflows, and implement the internal controls and system configurations needed to maintain continuous compliance without disruption to commercial operations.

Official Advisory Reference

The December 2024 GSTN advisory covering the January 2025 updates to the E-Way Bill and E-Invoice systems is available at the official GST portal: https://www.gst.gov.in/newsandupdates/read/561. Subsequent advisories are published on the GSTN newsroom and the E-Way Bill system’s release notes documentation.