Tokyo lodged an official protest with Moscow after the incident, saying two Russian Su-27 fighter jets had spent one minute and 11 seconds in Japanese airspace southwest of the island of Rishiri, not far from Hokkaido, Kyodo reported.
The incident took place near a set of four disputed islands to which both countries have laid claim since the end of World War II, called the Northern Territories in Japanese and considered part of the Kuril Islands by Russia.
Russian troops, planes and ships have been holding large-scale military drills on the Kurils since Wednesday.
"Flights by the Pacific Fleet’s naval aircraft take place regularly in this area and strictly adhere to international rules regarding the use of airspace, without violating the borders of other countries,” Captain 1st Rank Roman Martov, spokesman for Russia’s Eastern Military District, told RIA Novosti after the spat.
Tokyo has repeatedly accused Russian military planes of violating its airspace and Russia’s Defense Ministry has regularly denied the charges. Kyodo cited Japan’s Defense Ministry as saying the latest incident was "the first such intrusion in five years.”