Defense Ministry official Yoshihide Yoshida said Japanese air force jets scrambled after an intrusion by two Su-27 jets which lasted just over a minute.
Mr. Yoshida said it was not immediately known whether the incident was intentional or accidental, but that it was "extremely problematic." The last intrusion by Russian jets in Japanese airspace was on Feb. 9, 2008, he said.
In Moscow, the Russian Defense Ministry issued a statement denying any intrusion. It said Russian military aircraft taking part in a military exercise in the area flew in "strict conformity with international rules without any border violations."
It was not immediately clear whether the incident off the northwestern tip of Japan's Hokkaido island was related to Northern Territories Day.
Prime Minister Shinzo Abe told a government-sponsored rally in Tokyo that he will do his utmost to resolve the territorial dispute, which has kept the two nations from signing a peace treaty officially ending their hostilities in World War II.
Soviet troops captured the islands off Hokkaido's eastern coast in the waning days of the war, forcing about 17,000 Japanese residents to be deported over the next few years. About 17,000 people, mostly Russians, live there now.