On Saturday, Three Russian naval ships passed between Japan's two westernmost islands of Yonaguni and Iriomote.
From Friday through Saturday, a destroyer, frigate and supply ships sailed between the islands near Taiwan and moved into the East China Sea.
After analyzing the ships' actions and motives, the ministry presume the ships were traveling back to Russia.
Last month, Defense Minister Nobuo Kishi said that five Russian naval ships "almost encircled Japan," and three Chinese vessels followed a similar path.