The two Tu-95 planes breached airspace near the isle of Okinoshima off Fukuoka in southern Japan for nearly two minutes shortly after midday, a defence ministry spokesman said.
"A total of four F-2 planes from the Air Self-Defence Force scrambled against them," the official said.
The Japanese foreign ministry said it filed a formal protest with the Russian embassy in Tokyo over the violation and urged them to investigate it.
In February two Russian Su-27 fighters breached Japan's airspace for just over a minute off the northern island of Hokkaido, Japanese officials said at that time, in what was reported to be the first such incident in five years.
Japan is also at odds with China over the sovereignty of an island chain near Taiwan, in a particularly bitter dispute that has seen both sides scramble aircraft.