The incident occurred as Japan was observing "Northern Territories Day," when it holds annual rallies urging Moscow to return the islands, seized by the Soviet Union in the final days of World War II.
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.
Japan says a treaty dating back to Feb. 7, 1855, supports its claim to the islands, called the Northern Territories in Japan and the Southern Kurils in Russia.
They lie as close as six miles to Hokkaido and are also near undisputed Russian territory. The islands are surrounded by rich fishing grounds and are believed to have offshore oil and natural gas reserves, plus gold and silver deposits.
Addressing former Japanese residents of the islands and others gathered in a large Tokyo concert hall, Mr. Abe said he told Russian President Vladimir Putin in December that he wants to settle the dispute. Abe plans to send former Prime Minister Yoshiro Mori as a special envoy to Russia this month, but prospects for progress on the issue are uncertain.
"We aim to finally resolve the problem with Russia on the disputed islands and realize the signing of a peace treaty," Abe said in a brief speech before being whisked back to parliamentary proceedings.
In 2010, former President Dmitry Medvedev became the first Russian or Soviet leader to visit the islands, triggering sharp rebukes from Tokyo. He visited a second time last July.
More than half of the former Japanese residents of the islands have died in the 68 years since the Russians took control.
"My birthplace is right in front of me, but I can't return" to live there, said Choriki Sugawara, a 79-year-old man who recalled happy memories growing up on the island of Kunashir — called Kunashiri in Japan — in a fishing family of eight.