Washington and its allies are increasingly crossing the 180-kilometre (112-mile) Taiwan Strait to reinforce its status as an international waterway, angering Beijing.
The Sazanami destroyer made the passage on Wednesday at the same time as navy vessels from Australia and New Zealand, several Japanese media outlets said.
The three nations planned to conduct military drills in the South China Sea, the reports said. There was no immediate confirmation from the defence ministry.
Last week, China's Liaoning aircraft carrier sailed between two Japanese islands near Taiwan for the first time, accompanied by two destroyers.
Tokyo said the ships entered its contiguous zone -- an area up to 24 nautical miles from the Japanese coast -- and called the incident "totally unacceptable", while China said it had complied with international law.
It followed the first confirmed incursion into Japanese airspace by a Chinese surveillance aircraft in August.
On Thursday, the Yomiuri Shimbun daily cited unnamed government sources as saying Prime Minister Fumio Kishida had instructed the Taiwan Strait journey over concern that doing nothing following China's intrusion into Japanese territory could encourage Beijing to take more assertive actions.
Beijing views Taiwan as a renegade province and claims jurisdiction over the body of water that separates the island from China.
But the United States and many other countries argue their voyages are usual, citing freedom of navigation.
China this month accused Berlin of heightening security risks in the Taiwan Strait, a day after two German military vessels sailed through the waters.
The reported sailing comes as Kishida's ruling party holds a leadership election on Friday that will be a de facto vote to decide Japan's next prime minister, with candidates debating issues including regional security.
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 missile test, expressing "serious concern" about China's military build-up.
Beijing has said it would never renounce the use of force to bring Taiwan under its control, with Chinese leader Xi Jinping in recent years upping the rhetoric of "unification" being "inevitable".
In response, Taiwan has strengthened economic and political ties with its allies -- most notably the United States, its biggest weapons provider -- while increasing its defence budget.
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