The protest was made on Tuesday after the Russian media announced the construction of four barracks on the islands of Etorofu and Kunashiri -- the largest islands in southern Kuril, as well as plans to construct other military facilities, Efe news reported.
Japanese government spokesperson Yoshihide Suga said that Tokyo had used diplomatic channels to submit a formal protest with Russia and it would continue negotiations to resolve the issue and sign a peace treaty between the two countries.
Four islands of the archipelago's 56 were occupied during World War II by Russia, which has been involved in a dispute with Japan over their sovereignty ever since. The issue is a main point of contention between Moscow and Tokyo.
(With inputs from agencies.)