Chief Cabinet Secretary Yoshihide Suga told a press briefing on the matter that the drills are "unacceptable as it would lead to a stronger Russian military presence" on the disputed islands.
Suga, Japan's top government spokesperson, confirmed that Tokyo had lodged a protest with Moscow over the drills, but added that government of Prime Minister Shinzo Abe will "continue to strive to resolve the territorial issue and sign a peace treaty."
Japan was informed of the drills on Tuesday, the Foreign Ministry said, with notification given from Moscow that it would conduct military drills from Thursday to April 12 in waters east of southern Kunashiri Island.
The Ministry of Foreign Affairs of Japan has yet to confirm whether the drills, reportedly to involve live firing, have begun.
The island closest to where the drills are scheduled to take place is the southernmost of four islets central to a territorial dispute between Japan and Russia.
The islands are known as the Northern Territories in Japan and the Southern Kurils in Russia.
The decades-old territorial spat has prevented the two countries from signing a post-World War II peace treaty and hindered diplomatic and trade relations between the two countries.
Both parties have, however, provisionally agreed to discuss furthering joint economic activities on the islands.
Such activities span defense, search and rescue operations, medical areas, industry promotion and energy development, in line with a previously proposed plan, which also covers aquaculture and tourism.
The multi-faceted cooperation plan, based around five pillars proposed by Abe in 2016, was, purportedly, to become an important foundation for future ties.
Russia last held drills in March this year, however, on two of the disputed islands, involving tanks and around 500 military troops.
"We closely monitor the Russian military's movements in the Northern Territories on a regular basis," Suga also said Thursday.