Japan protested to Moscow after a Russian military plane intruded into Japanese air space over the Izu Islands south of Tokyo on Saturday, a Japanese foreign ministry official said.
The foreign ministry told the Russian government to investigate the case and sought an explanation, the official said.
The Russian warplane flew over the isle of Sofugan, about 650 km (400 miles) south of Tokyo, around 7:30 a.m. (10:30 p.m. British time on Friday), the official said.
"We strongly protest against the violation," the official said.
Russia last violated Japanese air space in January 2006, when a Russian plane flew over Rebun Island off the coast of Hokkaido, a major island in the north, the official said.
Kyodo news agency reported 22 Japanese fighter jets were scrambled to deal with the intrusion.
Japan and Russia have been locked in a decades-old territorial dispute that has prevented the two sides from signing a peace treaty putting a formal end to World War Two.
Despite the long-standing row, the two countries have been trying to expand ties. Russia is keen for funds to develop its far eastern regions, while Japan is eager to tap Russia's booming oil industry to reduce its reliance on Middle Eastern energy.
Russian President Vladimir Putin has offered new talks to resolve the territorial dispute, prompting Japanese Prime Minister Yasuo Fukuda to consider a visit to Moscow.
Fukuda said earlier in the week he had received a letter in which Putin had expressed his willingness to end the dispute.
