The Sazanami sailed south through the 180-kilometer 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 increased military activity by China around Japan.
The Sazanami entered the strait from the East China Sea on Wednesday morning and spent more than 10 hours sailing south to complete the passage, public broadcaster NHK and the Yomiuri Shimbun newspaper reported Thursday.
The voyage was carried out with Australian and New Zealand warships ahead of planned exercises in the disputed South China Sea, according to reports.
Japanese government spokesman Yoshimasa Hayashi declined to comment on the reports at a regular news conference because they concern military operations. There was no immediate confirmation from the Defense Ministry.
The New Zealand Navy confirmed that its ship, the HMNZS Aotearoa, had sailed through the strait with the Australian Navy's HMAS Sydney. A spokesman told AFP news agency that their first transit in seven years was to assert the “right to freedom of navigation”.
The three-ship transit comes a week after China's Liaoning aircraft carrier 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 had entered its contiguous zone, an area up to 24 nautical miles (about 44 kilometers) 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 southwest coast.
The Yomiuri Shimbun newspaper cited several unnamed government sources as saying that Prime Minister Fumio Kishida had ordered the Taiwan Strait transit out of fear that doing nothing in the face of Chinese activities could encourage Beijing to take more assertive action.
In Tokyo on Thursday, spokesman Hayashi expressed concern about China's increasing military activity in the region.
“We have a strong sense of crisis over the airspace violations that have occurred one after another in a short period of time,” he said at a regular press conference. “We will follow the situation with great interest.”
The United States and its allies send ships through the 180-kilometer (112-mile) strait to reinforce its status as an international waterway. Beijing claims it has jurisdiction over the waters and accused Germany of increasing 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 AFP that Japan's alleged transit of the Taiwan Strait was “part of a broader pattern of increased naval presence by countries in and outside Asia that are concerned about China's maritime claims.”
“Japan in particular has been grappling with China’s ‘grey zone’ tactics in the East China Sea,” including an increasing number of coast guard vessels sailing near disputed islands, he said.
Gray zone tactics are actions that serve to exhaust a country's armed forces, according to military experts.
China on Wednesday test-fired an intercontinental ballistic missile into the Pacific Ocean in its first such exercise in decades.
Japan said it had received no advance notice of the test and expressed “serious concern” about China’s military buildup.
Leaders of the Quad group of Australia, India, Japan and the United States last week expanded joint security measures in Asian waters over shared concerns about China.
