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Russia has been holding military manoeuvres around the disputed Kurile islands this week.
"Flights of military aircraft are ... carried out in strict accordance with the international rules governing air space and do not violate the border of other states," a Defence Ministry spokesman, Colonel Alexander Gordeyev, told Interfax news agency.
"All flights by the air forces in the region are strictly regulated by the joint command and are carried out under the supervision of air traffic control," said Gordeyev, the spokesman for Russia's Eastern Military District.
Thursday was Japan's "Northern Territories Day", when rallies are traditionally held calling for the return of disputed islands off Hokkaido and are likely to heighten tensions with Russia over the contested territories.