Four Chinese coastguard ships briefly sailed through Taiwan's "prohibited" waters, Taipei said, urging Beijing to stop actions that "endanger" navigation safety.
China claims self-ruled democratic Taiwan as part of its territory, and has said it will not rule out using force to bring the island under Beijing's control.
The Chinese ships entered waters south of Taiwan's outlying island of Kinmen, five kilometres (three miles) from the Chinese city of Xiamen, around 3:30 pm (0730 GMT) on Monday, Taiwan's coastguard said in a statement later the same day.
The ships "sailed out of our prohibited and restricted waters" about an hour later, the agency said, urging Beijing to immediately stop "behaviour that endangers navigation safety".
The sorties come weeks before the May 20 inauguration of new Taiwan president Lai Ching-te, who China regards as a dangerous separatist.
Like outgoing President Tsai Ing-wen, Lai rejects China's claim on Taiwan.
Beijing had also vowed to step up patrols around Kinmen, which is administered by Taipei, after a series of deadly fishing accidents earlier this year.
A Chinese speedboat carrying four people capsized near Kinmen on February 14 while Taiwan's coastguard was pursuing it, leaving two dead.
Another Chinese boat capsized in the area in March, also resulting in the death of two crew members.
Taiwan's coastguard had defended its actions, saying the boat was within "prohibited waters" and was zigzagging before it capsized, but Beijing accused Taipei of "hiding the truth" about the incident.
Defence ministry spokesman Sun Li-fang told reporters Tuesday during a flag-raising rehearsal for the May 20 inauguration that Taiwan would boost support to the coastguard in the form of surveillance and reconnaissance.
When asked if the presence of Chinese ships would disrupt the shipping of supplies to Taiwan's offshore islands, he said "overall we are very well prepared and have full confidence in ensuring regional security".
He added that "there is no abnormality in the Taiwan Strait at the moment".
"We have made the most complete preparations taking into account the enemy's threats and can cope with any unexpected situation," Sun said.
Given the heightened tensions, Taiwanese authorities said they were on alert for potential military exercises by Beijing after May 20.
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