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".
China has in recent years ramped up sorties of aircraft and naval vessels around the island.
Monday's incident comes two weeks before the May 20 inauguration of Taiwan's president-elect Lai Ching-te.
Like outgoing President Tsai Ing-wen, Lai rejects China's claim on Taiwan.
Beijing considers Lai, who is currently vice president, a "dangerous separatist" who will lead Taiwan down a path of "war and decline".
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 that Taiwan would boost support to the coastguard in the form of surveillance and reconnaissance of Chinese ships entering the island's restricted waters.
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".
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