Tokyo will not be deterred and will continue with its plans to let a Japanese warship sailed through the Taiwan Strait for the first time. No details were made available as top government spokesman Yoshimasa Hayashi declined to comment on the reports at a regular briefing because they concerned military operations.
However, 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 25 September, 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 26 September.
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.