Lithuania ERP and accounting: i.SAF, i.MAS, SAF-T and VAT

Lithuanian compliance in one view

Lithuania has no general B2B e-invoicing mandate, but its tax authority already sees invoice-level data. Every month, VAT-registered companies send the details of each invoice they issue and receive to VMI's i.SAF system, file a VAT return by the 25th, send e-invoices to the public sector through SABIS, and must be able to export their accounting data as a SAF-T file. It matters because Lithuanian VAT is checked invoice by invoice.

Tax administration is national. The State Tax Inspectorate (VMI), under the Ministry of Finance, runs VAT, corporate and personal income tax and the smart tax administration system i.MAS. Declarations go through the Electronic Declaration System (EDS), and taxpayers see their obligations in My VMI. Social insurance is administered separately by Sodra, the State Social Insurance Fund Board.

This page explains why Lithuania built i.MAS, how its reporting works, every dated step as of September 2026, and what Skyline Nexus ERP does for a Lithuanian business.

• Tax authority: VMI, through EDS, My VMI and i.MAS
• Currency: euro; standard VAT rate 21%
• Invoice data: monthly to i.SAF since 1 October 2016
• B2G e-invoicing: mandatory since 1 July 2017, via SABIS
• B2B e-invoicing: not mandatory as of September 2026

Why Lithuania built i.MAS and i.SAF

Lithuania's reform began with the VAT gap: the difference between the VAT a country should collect and what it actually collects, which the European Commission estimates every year for each member state. Rather than start with a clearance model, VMI built a smart tax administration system, i.MAS, that collects structured data it can analyse: invoice registers through i.SAF, electronic waybills for goods in transit through i.VAZ, and accounting data files through i.SAF-T.

i.SAF is the part most businesses meet every month. Because both the supplier and the buyer report the same invoice, VMI can cross-check them automatically, find invoices reported on only one side or with different amounts, and show those discrepancies to the taxpayer in the system. The same data lets VMI prepare preliminary VAT returns, so reporting also saves work.

The SAF-T project had a similar logic for audits. VMI describes its aim as replacing inconvenient paper submissions with standardised files, shortening inspections, applying the same checks to every taxpayer and basing conclusions on all of a company's data rather than a selected sample.

How i.SAF, i.VAZ and i.SAF-T work

A company creates a register for each tax period in i.SAF and either enters invoice data directly in the portal, uploads an XML file with its issued and received VAT invoices, or sends the data automatically through web services from its accounting software. VMI publishes the XML technical specification and the web service specification. Payment data can be added, but is optional.

i.SAF also offers taxpayers useful tools: individuals can issue e-invoices in the portal, companies can receive and view e-invoices, an e-waybill can be created from an e-invoice, preliminary FR0600 returns and FR0564 reports can be ordered, and discrepancies found by cross-checking can be reviewed. i.VAZ handles e-waybills for goods transport, and i.SAF-T receives SAF-T accounting files, including large files through a dedicated file transfer tool.

For an accounting system, the practical requirement is that every VAT invoice is held with the data i.SAF expects, including the partner's VAT code, invoice number and date, taxable value and VAT by rate, and that received invoices are recorded promptly enough to be reported on time.

• i.SAF: monthly registers of issued and received VAT invoices
• Channels: portal entry, XML upload or web services
• Cross-checking: supplier and buyer data matched by VMI
• i.VAZ: electronic waybills for goods in transit
• i.SAF-T: OECD-standard accounting data files

Deadlines: every dated step as of September 2026

The dates below come from VMI's pages and the consolidated VAT Act published on the Seimas legal register, and from the European Commission's country page. They describe the position as of September 2026. The European Commission's page reports that mandatory B2B e-invoicing is targeted for 1 January 2028 to align with the EU's VAT in the Digital Age package, but no domestic B2B mandate has taken effect, so we do not treat that as a deadline yet; confirm the status with VMI before planning around it.

• 1 October 2016: VAT invoice register data submitted to VMI through i.SAF
• 1 July 2017: e-invoicing mandatory for suppliers to contracting authorities
• November 2020: the i.SAF-T subsystem for SAF-T accounting files completed
• September 2024: SABIS becomes the only accepted channel for B2G e-invoices
• 1 May 2025: new rules for VAT payers using the small business scheme (SVS)
• June 2025: VAT Act amendments reshape the 12% and 5% reduced rates
• 20th of each month: i.SAF registers; 25th: FR0600 VAT return and FR0564 report
• 1 July 2030: EU-wide e-invoicing and digital reporting for intra-EU B2B supplies under ViDA

VAT rates, registration and returns

The standard rate is 21%. Under Article 19 of the VAT Act, as amended in June 2025 and consolidated for 2026, the 12% rate applies to accommodation services provided under tourism rules, passenger and luggage transport on scheduled routes set by the Ministry of Transport or municipalities, and admission to art and cultural institutions and events. The 5% rate applies to reimbursed medicines, medical aids and special medical foods, non-reimbursed prescription medicines, technical aids for people with disabilities and their repair, newspapers, magazines and other periodicals, and printed and electronic books and non-periodical information publications.

A Lithuanian taxable person must register for VAT once its supplies in the country over the last 12 months exceed 45,000 euro, or earlier if its acquisitions of goods from other member states exceed 14,000 euro. Foreign taxable persons must register from the start of their economic activity in Lithuania.

The FR0600 return is filed in EDS by the 25th day of the month after the period: monthly for legal persons, or quarterly on request below 300,000 euro of revenue without taxable EU acquisitions, and half-yearly for individuals by default. The FR0564 report on supplies to EU VAT payers is due by the same day for the months in which such supplies were made.

• 21% standard rate
• 12%: accommodation, scheduled passenger transport, cultural events
• 5%: medicines, disability aids, periodicals, books
• Registration above 45,000 euro in 12 months

Accounting framework and record keeping

Lithuanian companies keep their books under the Law on Financial Accounting and prepare financial statements under the national Business Accounting Standards (VAS), while listed groups prepare consolidated accounts under IFRS as adopted in the EU. The financial year normally follows the calendar year, and annual financial statements are filed with the Register of Legal Entities.

Because VMI's inspections increasingly start from data, the practical standard for record keeping is set by i.SAF and SAF-T as much as by law. A company should be able to show, for any period, the invoice registers it reported, the ledger that produced them and a SAF-T export that ties to both. Records must be kept for the periods set by the accounting and archives legislation, and for as long as a tax inspection could still reach the period.

Cash is also watched: VMI publishes rules on cash settlements, and retail cash registers are covered by their own requirements, so cash takings should reach the ledger as daily totals reconciled to the register.

Payroll: VMI and Sodra

Employers withhold personal income tax from salaries and declare and pay it to VMI, and they declare and pay social insurance contributions to Sodra, the State Social Insurance Fund Board. Health insurance contributions are part of that system too. The two institutions receive separate declarations, so payroll software must produce both and the ledger must hold separate liabilities for each.

For the ledger, that means a payroll journal each month with liabilities for income tax, social insurance and health insurance, reconciled to what was declared to VMI and Sodra and what was paid.

Cities and regions: where the rules differ

VAT, i.SAF, income tax and social insurance are national, so a business in Vilnius, Kaunas, Klaipėda, Šiauliai, Panevėžys, Alytus, Marijampolė, Mažeikiai or Utena reports and files under the same rules and deadlines. There is no regional VAT rate or e-invoicing regime.

What differs is local. Municipalities set real estate and land tax rates within national limits, and Lithuania has free economic zones, for example in Kaunas and Klaipėda, where companies that meet the investment conditions can receive corporate tax relief. A group with one company inside a free economic zone and another outside it needs clean intercompany accounting, because the relief depends on the zone company's own results.

• Real estate and land tax: rates set by municipalities
• Free economic zones: corporate tax relief for qualifying companies
• VAT, i.SAF and payroll: identical nationwide

How Skyline Nexus ERP handles Lithuanian requirements

Skyline Nexus ERP is a cloud ERP with a double-entry general ledger under Fiscal Authority. With the auto-post switches on, final sales, purchases, payments, expenses and depreciation post balanced journals in the background, and output VAT is computed per line on the same basis as the tax report, so 21%, 12% and 5% lines each post correctly. The VAT Return screen prefills tax-exclusive sales and purchase bases and VAT for a date range and location for the FR0600, and the VAT Analysis report lists input and output VAT from the ledger, the natural starting point for reconciling i.SAF registers to the books.

Corrections follow the rules: posted journals are reversed rather than edited, sales returns are recorded as credit notes, fiscal periods can be soft-closed or locked, and the Accounting Audit Trail records who changed what, with old and new values. The Audit Pack exports a year's chart of accounts, trial balance, ledger, journal lines, sales, purchases and VAT summary to one Excel workbook, which an accountant can use as the working source for an inspection, and the chart of accounts can be imported from CSV or Excel.

National reporting and e-invoicing connectors are being rolled out market by market, and Lithuania's i.SAF, SAF-T and SABIS formats are part of that programme: tell us your country and we will confirm your go-live date. Until then, a partner-led integration can read sales and sales returns through the Skyline Nexus ERP Connector REST API for i.SAF and SABIS, alongside the Excel exports. Lithuanian payroll runs in local payroll software or through a payroll partner, with the payroll journal posted to the ledger each month.

Rates, regimes and deadlines in this summary change, and many countries are actively legislating on e-invoicing. This is general information, not tax or legal advice — confirm the current position with the authority named above or with your tax adviser before you rely on it.