One Russian aircraft travelled from Japan's north down along part of its west coast, while the other took a similar route along the opposite coast and returned the same way, the Joint Staff said in a brief statement.
"In response, fighters of the Air Self-Defense Force's Northern Air Force and other units were scrambled," it added.
There was no further information on the incident, which comes days after Japan hosted Ukrainian President Volodymyr Zelensky at the G7 in Hiroshima.
Japan has joined Western allies in sanctioning Moscow over its invasion of Ukraine, and has warned of the threat posed by Russia.
Its latest security document, which once called for enhanced ties and cooperation with Russia, now warns that Moscow's military posturing in Asia and cooperation with China are "a strong security concern".
In May 2022, Chinese and Russian military jets carried out joint flights near Japan immediately after a meeting of the US-led Quad grouping in Tokyo.
And more recently Moscow has carried out military exercises including test-firing missiles in the Sea of Japan.
Russia considers Japan to be a "hostile" country -- a designation it shares with all European Union countries, the United States and its allies, including Britain and Australia.
Tokyo had complex relations with Moscow before the invasion of Ukraine in February, and the two sides have yet to sign a post-World War II peace treaty.
Attempts to do so have been hampered by a long-running dispute over islands controlled by Russia, which calls them the Kurils.
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