The Japan Maritime Self-Defense Force vessel Sazanami made the transit alongside ships from Australia and New Zealand on Wednesday. The narrow waterway separates China from Taiwan, which Beijing claims as its own territory.
The passage comes amid escalating regional tensions, with China intensifying its military activities around Japan. In late August, a Chinese surveillance aircraft violated Japanese airspace near islands in Nagasaki Prefecture.
Earlier this month, a Chinese aircraft carrier entered the contiguous zone just outside Japan's territorial waters for the first time, sailing between remote islands in southern Japan from the East China Sea.
The United States regularly conducts freedom of navigation operations through the Taiwan Strait, with allies such as Britain and Australia also making similar passages in recent years, drawing criticism from China. Beijing views Taiwan as a breakaway province to be reunified with the mainland, by force if necessary.