Two IL-38 planes flew along shorelines of Hokkaido, Aomori and Akita, facing the Sea of Japan (East Sea), but stayed away from Japanese airspace, the ministry added.
Japan's Self-Defence Forces "responded by scrambling fighters," according to a brief press release from the ministry which came with a map of the Russian planes' flight path.
Japanese defence officials could not be reached for immediate comment.
The incident came only days after Russian bombers briefly intruded into the Japanese airspace Thursday, prompting Tokyo to scramble fighter jets.
Also Read
A total of four F-2 fighter jets from the Air Self-Defence Force scrambled against them, a defence ministry official said at the time.
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 Hokkaido 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.