Japan lodged a protest after the planes were detected off the northern island of Hokkaido for just over a minute.
The incident happened after Japanese PM Shinzo Abe said he was seeking a solution to a territorial dispute with Russia over a Pacific island chain.
Russia’s military denied the incursion, saying the jets were making routine flights near the disputed islands.
Shinzo Abe was speaking on the anniversary of an 1855 treaty which Japan says supports its claims to the islands.
The four islands – which Russia calls the Southern Kurils and Japan calls the Northern Territories – are the subject of a 60-year-old dispute.
Because of the dispute, the two nations have not yet signed a peace treaty to end World War II.
“Today, around 03:00, military fighters belonging to Russian Federation breached our nation’s airspace above territorial waters off Rishiri island in Hokkaido,” the foreign ministry said, quoted by AFP news agency.
Hours earlier, Shinzo Abe told former inhabitants of the disputed islands and their descendents: “In the telephone talks, I told [Russian] President [Vladimir] Putin I would make efforts to find a mutually acceptable solution so as to ultimately solve the issue of the Northern Territories.”
In December, Shinzo Abe and Vladimir Putin agreed to restart talks on signing a peace treaty.
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