Taiwan, which China claims as its own territory, has complained of regular such missions by the Chinese air force over the last two years, though the aircraft do not get close to Taiwan itself.
The number of aircraft involved was well off the last large-scale incursion, 39 Chinese aircraft on Jan. 23, and since then, such fly-bys have been sporadic with far fewer aircraft.
The ministry said the latest mission involved eight Chinese J-16 fighters and one Y-8 reconnaissance aircraft, which flew over an area to the northeast of the Taiwan-controlled Pratas Islands at the top end of the South China Sea.
Taiwanese fighters were sent up to warn the Chinese aircraft and air defense missiles were deployed to "monitor the activities," the ministry said, using standard wording for how Taiwan describes its response.
While Taipei has not reported any unusual movements by Chinese forces, the government has increased its alert level.
China has never renounced the use of force to bring Taiwan under its control, and routinely condemns US arms sales or other shows of support from Washington.
"We urge the US side to recognize the high sensitivity of the Taiwan issue, stop interfering in China's internal affairs and stop playing with fire on the Taiwan issue," Tan said.
In the 12-page Indo-Pacific strategy overview issued earlier this month, the Biden administration vowed to commit more diplomatic and security resources to the region.
On Taiwan, Washington would work with partners inside and outside the region to maintain peace and stability in the strait dividing the island from China, it said.