The Sazanami sailed south through the 180-kilometre waterway with ships from Australia and New Zealand.
Japan has sent a destroyer through the Taiwan Strait for the first time, Japanese media reported, amid increasing military activity around Japan by China.
The Sazanami entered the strait from the East China Sea on Wednesday morning, spending more than 10 hours sailing south to complete the passage, public broadcaster NHK and the Yomiuri Shimbun newspaper reported on Thursday.
The passage was conducted with naval ships from Australia and New Zealand ahead of planned drills in the disputed South China Sea, the reports said.
Japan’s top government spokesman Yoshimasa Hayashi declined to comment on the reports at a regular briefing because they concerned military operations. There was no immediate confirmation from the Ministry of Defence.
The transit comes a week after the Chinese aircraft carrier Liaoning sailed for the first time between two Japanese islands near Taiwan, a self-ruled democracy that Beijing claims as its own.
Tokyo said the ships entered its contiguous zone, an area up to 24 nautical miles (about 44km) from the Japanese coast, and called the incident “totally unacceptable”. China said it had complied with international law.
In late August, Tokyo said a Chinese spy plane violated Japanese airspace near islands off its southwestern coast.
The Yomiuri Shimbun cited multiple unnamed government sources as saying Prime Minister Fumio Kishida had ordered the Taiwan Strait transit over concern that doing nothing in the wake of the Chinese activities could encourage Beijing to take more assertive actions.
The United States and its allies send ships through the 180-kilometre (112-mile) strait to reinforce its status as an international waterway. Beijing claims it has jurisdiction over the waters and accused Germany of heightening security risks after Berlin sent two of its military vessels through the strait last month.
Bec Strating, a professor of international relations at La Trobe University, told the AFP news agency Japan’s reported Taiwan Strait transit was “part of a broader pattern of greater naval presence by countries in and beyond Asia that are concerned about China’s maritime assertions.
“Japan in particular has been dealing with China’s ‘grey zone’ tactics in the East China Sea,” including an increasing number of coastguard vessels sailing close to disputed islands, she said.
Grey-zone tactics are actions that serve to exhaust a country’s armed forces, according to military experts.
On Wednesday, China test-launched an intercontinental ballistic missile into the Pacific Ocean in its first such exercise in decades.
Japan said it had not been given advance notice of the test, and expressed “serious concern” over China’s military build-up.
Leaders of the Quad grouping of Australia, India, Japan and the United States last week expanded joint security steps in Asia’s waters due to shared concerns about China.