The note of protest was sent to the Russian Foreign Ministry through the Japanese Embassy to Moscow on August 3, according to Suga.
Japanese media reported earlier that Russian Su-35 fighter jets were deployed for a guard duty to the Iturup island, part of the Kurils archipelago.
"We have asked the Russian side to take certain measures in connection with the fact that Russia is boosting its military presence on the four disputed islands, with Russian military equipment being also very active [in the area]. Russia is our important neighbor, and we hope that maintenance of dialogue and cooperation will prevent ad hoc situations and unnecessary tensions," the Japanese minister explained.
In February, the Russian government released a decree stipulating that the Russian Aerospace Forces' combat jets and civil aircraft would be jointly based on Iturup, one of the disputed Kuril Islands.
The Russian-Japanese relations have long been complicated by the fact that the two nations have never signed a permanent peace treaty after the end of World War II. The deal was never reached because of a disagreement over a group of four islands that are claimed by both countries: Iturup, Kunashir, Shikotan and Habomai.