Two Russian fighters briefly intruded into Japanese airspace off the northern tip of the island of Hokkaido, the defence ministry says.
Japanese air force jets scrambled after the intrusion by the two SU-27 jets off the coast of Rishiri island.
An official said it was not immediately known whether the airspace violation was intentional or accidental, but that it was "extremely problematic."
He says the last intrusion by Russian jets in Japanese airspace was in February 2008.
Later the Russian defence ministry denied the claims, It said Russian military aircraft taking part in today's military exercise in the area flew in "strict conformity with international rules without any border violations"
The two countries are locked in a long-running dispute over a chain of islands in the Pacific.
Japan's Foreign Ministry lodged a protest with the Russian Embassy in Tokyo.
It was not clear whether the incident was related to a government-sponsored rally held today demanding that Moscow return the group of disputed islands off Hokkaido's eastern coast.
Prime Minister Shinzo Abe told the rally that he will do his utmost to resolve the dispute with Russia, which has kept the two nations from signing a peace treaty officially ending their hostilities in the Second World War.