The Russian government denied any violation of Japanese airspace, The Japan Press reported. Officials said the jets were participating in military maneuvers near the Kuril Islands, which Russia has occupied since World War II.
Japan claims the Kurils, calling them the Northern Territories.
Prime Minister Shinzo Abe said Thursday he hopes negotiations would resolve the question of sovereignty.
The Japanese foreign ministry said four Japanese F-2 fighter jets were scrambled after the two Russian SU-27 fighters spent less than a minute in Japanese airspace, The Wall Street Journal reported.
Japan is involved in a similar territorial dispute with China.
Narushige Michishita, a Northeast Asia security expert at Japan's National Graduate Institute for Policy Studies, suggested Russia is taking advantage of that.
"Certainly, they are testing us and using the opportunity created by the Chinese diversion," he said "The Russians know that whatever they do, it will not look as bad as what the Chinese are doing."
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