The Interpol office in the Baltic state said Viktor Uspaskich, 47, an ex-economy minister and former Labor Party leader wanted on suspicion of defrauding party finances, was arrested in Moscow September 15.
But the Prosecutor General's Office in Russia denied the arrest had happened and also said Lithuania had not filed any arrest or extradition requests with regard to Uspaskich.
Lithuanian authorities put Uspaskich, who is also accused of receiving funds from Russia's security services, on the international wanted list after he failed to turn up for questioning. His party offices and apartment were searched in late May.
Uspaskich, who has been living in Russia since May, has dismissed the accusations as politically motivated.
The businessman was elected to parliament in 2000. In 2003, he founded the Labor Party, which won a decisive victory in parliamentary elections the next year. In mid-2005, Uspaskich resigned as economy minister in the cabinet formed after the elections and later quit as party leader.