The Russian Defense Ministry said the plane crashed near a village in western Lithuania 30 kilometers away from the border with Kaliningrad, Russia's exclave on the Baltic Sea.
The Lithuanian Defense Ministry said the crash site was further to the south, and the incident had been caused when two Russian planes collided.
The two sides said no one had been hurt and no major damage had been inflicted.
A Russian spokesman said the condition of the pilot, Major Valery Troyanov, who ejected from the plane, was satisfactory and he was now at a local police station.
He added that Major General Vladimir Sviridov, the commander of the 6th air force and air defense army that operated the plane, was in talks with Lithuania over a Russian official's flying to the site.
