Japan's top government spokesman Yoshimasa Hayashi declined to comment on the reports at a regular briefing because they concerned military operations.
But Beijing confirmed its military had responded to "the activities of a Japanese Self-Defence Force ship entering the Taiwan Strait".
"China is highly vigilant about the political intentions of Japan's actions and has lodged stern representations with Japan," foreign ministry spokesman Lin Jian said.
The United States and its allies are increasingly crossing through the 180-kilometre (112-mile) Taiwan Strait to reinforce its status as an international waterway, angering China.
The Sazanami destroyer made the unprecedented passage on Wednesday, several Japanese media outlets said.
Military vessels from New Zealand and Australia also sailed through the fiercely contested waterway on the same day, Wellington's defence ministry said on Thursday.
A defence official told AFP that one of its ships made its first passage through the Taiwan Strait in seven years, alongside an Australian guided missile destroyer to assert the "right of freedom of navigation".
The official added the mission was not conducted with Japan.
Japanese media said the three nations planned to conduct military drills in the contested South China Sea.
China's defence ministry also confirmed Thursday that vessels from the three countries "had a transit operation through the Taiwan Strait".
The Chinese military "stayed on high alert and monitored these passages", spokesman Zhang Xiaogang said.
"These operations will undermine China's sovereignty and security," he said.
"The (Chinese military) will remain on high alert and take all necessary measures to counter these threats and provocations," he added.
- 'Threaten' China -
In response to the "foreign warships transiting the Taiwan Strait", Beijing on Thursday said it "consistently handles such matters in accordance with laws and regulations".
The foreign ministry said it remained "highly vigilant against any actions that may threaten China's sovereignty and security".
Last week, China's Liaoning aircraft carrier sailed between two Japanese islands near Taiwan for the first time, accompanied by two destroyers.
The ships entered Japan's contiguous zone -- an area up to 24 nautical miles from the country's coast -- Tokyo said, calling the incident "totally unacceptable". China said it had complied with international law.
It followed the first confirmed incursion into Japanese airspace by a Chinese surveillance aircraft in August.
The Yomiuri Shimbun daily cited unnamed government sources as saying Prime Minister Fumio Kishida had ordered Wednesday's Taiwan Strait journey out of concern that doing nothing following China's intrusions could encourage Beijing to take more assertive actions.
- 'Serious concern' -
Beijing, which says democratic Taiwan is part of its territory, claims jurisdiction over the body of water that separates the island from China.
But the United States and many other countries argue their voyages through the strait are routine, citing freedom of navigation.
China this month accused Berlin of heightening security risks in the Taiwan Strait, a day after two German navy ships sailed through the waters.
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, with Hayashi expressing "serious concern" about China's military build-up in comments he reiterated on Thursday.
"China's military intrusion into our territorial airspace and other incidents have been happening one after another in a short period of time," Hayashi said.
Japan will do its "utmost in patrolling and monitoring" the situation, he added.
Taiwan's defence ministry also said Thursday that 43 Chinese military aircraft and eight naval vessels were detected around the island within a 24-hour period.
Beijing has said it will 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".
Bec Strating, professor of international relations at La Trobe University, said Japan's reported Taiwan Strait transit "is 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 coast guard vessels sailing close to disputed islands, she told AFP.
Grey-zone tactics are actions that serve to exhaust a country's armed forces, military experts say.
New Zealand navy sailed Taiwan Strait for first time in years
Wellington (AFP) Sept 26, 2024 -
New Zealand's navy said on Thursday that it had sailed a military vessel through the Taiwan Strait for the first time in seven years, a rare challenge to China's claim on the fiercely contested waterway.
A defence official told AFP that the HMNZS Aotearoa a relief ship sailed through the strait on Wednesday with an Australian guided missile destroyer, the HMAS Sydney.
"This was a routine activity, consistent with international law, including the right of freedom of navigation," a defence spokesperson said.
The United States and allied militaries regularly sail through the Taiwan Strait to assert their freedom of navigation.
Beijing views self-governing Taiwan as a renegade province and claims jurisdiction over the body of water that separates the island from China.
New Zealand -- which has deep trade ties with China -- has carried out military operations in the South China Sea but generally shies away from exercises in the Taiwan Strait.
The last time a New Zealand navy vessel passed through the strait was while sailing to the Chinese port of Qingdao in 2017, the defence official said.
Wednesday's mission was not conducted with Japan, which reportedly also sailed a warship through the strait for the first time.
"It was not done with a Japanese ship," the defence official said.
Since coming to office last year, New Zealand's centre-right government has pivoted hard toward "traditional allies" like the United States, Britain and Australia, and become much more vocal in its criticism of Beijing.
On Wednesday New Zealand issued an unusually strong condemnation of China's decision to launch an intercontinental ballistic missile that terminated in the South Pacific.
Wellington said that test, the first of its kind in decades, was "unwelcome and concerning".
In March, Wellington said a Chinese "state-sponsored group" was behind a 2021 malicious cyber attack that infiltrated sensitive government computer systems.
New Zealand is currently carrying out plans to shake up its defence forces and "reset" its foreign policy.
New Zealand is also mulling participation in AUKUS efforts to develop advanced military technology such as artificial intelligence, undersea drones, and hypersonic missiles.
AUKUS currently groups Australia, the United Kingdom and the United States.
High-profile New Zealanders such as former prime minister Helen Clark have warned against irking China and an increasing dependence on the United States.
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