The investigation will check how support money from international football bodies to Lithuania was used by the federation, Prime Minister Algirdas Butkevicius told reporters.
"The suspected amount is about several million euros. We are searching for documents which would confirm this and the schemes for their embezzlement", Kestutis Jucevicius, chief of the financial authority told LRT public broadcaster.
Edvinas Eimontas, CEO of the football federation, told Reuters he denies any embezzlement was going on. The federation runs Lithuanian national football team and organises international matches in Lithuania.
No charges were filed in the investigation, which started last month after a tip-off by Lithuanian parliament members, Jucevicius told reporters.
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His officers searched offices of the federation, home of its president Julius Kvedaras and four other locations.
The prime minister this week ordered a separate investigation by a government department to check whether the federation should be banned from receiving support from state budget.
The Lithuanian national football team, which is due to play England and Scotland in the World Cup 2018 qualifiers, this year dropped to 126 place in FIFA world rankings of 209 men's sides, its lowest result since the ranking was introduced in 1993.
(Reporting By Andrius Sytas Editing by Jeremy Gaunt)
