Taiwan alleges that fighter jets were ordered into its air defence zone to warn off 30 Chinese warplanes.
Monday’s intrusion was the most serious since January.
It happened just days after US Vice President Joe Biden warned China against invading Taiwan and on the same day that a senior US diplomat visited the island to discuss security with local officials.
China has increased the frequency of its aviation operations in recent months, claiming that they are training drills.
Taiwan has been incensed by such measures, which have heightened regional tensions.
China considers Taiwan to be a breakaway province that it can take by force if necessary.
The plane passed through an area northeast of the Pratas Islands that is part of Taiwan’s air defence identification zone, according to a chart provided by the ministry (ADIZ). The jets did not, however, fly into Taiwanese airspace, which would have been considered an act of aggression.
An ADIZ is a zone outside of a country’s borders and national airspace where foreign aircraft are detected, monitored, and controlled for national security reasons. It is self-declared and, in principle, preserves international airspace.
Taiwan has been reporting Chinese aircraft straying into its ADIZ for more than a year, describing it as “grey zone” warfare aimed at testing and exhausting its military response.
Mr Biden acknowledged the aviation incursions during his trip to Asia last week, which was his first visit to the region as president.
He cautioned China that it was “already flirting with danger right now by flying so close” to Taiwan, and he issued his most severe warning yet, implying that if Beijing seized the island, the US would be likely to respond militarily.
China’s military declared last week that it had just completed a practice over Taiwan as a “serious warning” against “collusion” with the United States.
The incursion took place on Monday when US Senator Tammy Duckworth arrived in Taipei on an unannounced visit to talk with Taiwanese President Tsai Ing-wen about regional security and trade concerns.