Lithuanian media quoting the prosecutors said the pilot, Major Valery Troyanov, was now considered a "suspect."
Earlier in the day he was questioned by the prosecutors for five hours in the presence of a Russian diplomat.
Lithuanian Defense Minister Gediminas Kirkilas said in a local radio interview that tentative investigation showed the reason of the crash Thursday was "a failure in the navigation equipment."
In an interview with the Russian radio station, Mayak, Kirkilas said: "We know that the plane flew into our territory giving a SOS signal. Russian Defense Minister Sergei Ivanov says the same. We hope further investigation will confirm it," he said.
The Su-27 was flying over the neutral waters of the Baltic Sea from St. Petersburg to Kaliningrad, a Russian exclave between European Union and NATO member countries Poland and Lithuania when it veered off course into Lithuanian airspace, according to the Lithuanian Defense Ministry.
The pilot ejected from the plane and landed 55 kilometers (34 miles) away from Kaunas, Lithuania's second largest city. He spent the night in the hospital where he underwent medical examination.
Earlier on Friday, Ivanov urged his Lithuanian counterpart to allow the pilot to return home "as soon as possible."
John Colston, NATO's assistant secretary general for defense policy, said NATO closely watched the investigation and was informed that Russia and Lithuania were trying to cooperate on the issue.
