According to the court, Filipchenko used false documents to conceal his true identity and repeatedly crossed the country's border illegally.
The Russian, who wore a grey suit and was guarded by four armed officers, calmly listened to the verdict and told the court that he understood it.
According to the State Security Department, this is the first time that a sworn officer of the Russian security service has been detained in Lithuania for spying.
Lithuanian law-enforcement officials have said that Filipchenko sought to recruit officers from Lithuania's VIP Protection Department to bug the office and home of President Dalia Grybauskaitė.
Neither the judge nor the prosecutor commented on the circumstances on Friday.
The judge said that the Russian citizen had refused to testify in the case. The man did not answer reporters' questions as he was escorted out of the court.
The sentence can be appealed to the Lithuanian Court of Appeals within 20 days.