The Kinmen islands are administered by Taipei but located just five kilometres (three miles) from the Chinese mainland.
Last month, two men died when a Chinese fishing boat capsized nearby while being pursued by Taiwan's coast guard, sparking a heated argument between the two sides.
Another Chinese boat capsized in the area on Thursday, also resulting in the death of two crew members.
There was no indication the boat was being pursued, and the sinking prompted a joint rescue operation by China and Taiwan.
The Chinese coast guard said in a statement Friday it had patrolled the waters around the Kinmen islands that day "in accordance with the law".
"The coast guard will continue to step up patrols to safeguard the legitimate rights and interests, as well as the safety and property, of Chinese fishermen, including those from Taiwan," it said.
Beijing claims self-ruled Taiwan as its own territory and has vowed to take it one day, by force if necessary.
Since the first fatal incident on February 14, an average of six to seven Chinese vessels have been seen daily in waters around Kinmen, Taiwan's coast guard chief said.
That capsizing further strained cross-strait relations, after a survivor reportedly said the boat was "rammed".
But Taiwan insisted its coast guard was following legitimate procedures after the vessel entered "prohibited waters".
It said the boat involved was zigzagging, "lost its balance and capsized" while trying to evade the Taiwanese patrol.
Beijing has accused Taiwan of "seeking to evade their responsibilities and hide the truth" about the incident.
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