A further 26 aircraft -- including fighters, transport planes and drones -- were detected after 6:55 am (2255 GMT) Friday, the ministry said.
China claims self-ruled democratic Taiwan as part of its territory and has said it would never renounce the use of force to bring it under Beijing's control.
It has stepped up pressure on Taipei in recent years and held war games around the island following the May 20 inauguration of new Taiwanese leader Lai Ching-te, who Beijing regards as a "dangerous separatist".
During those drills, Beijing sent 62 military aircraft around Taiwan -- the highest single-day total this year -- as well as 27 naval vessels, according to Taipei's defence ministry.
On Friday, the ministry said it had detected 36 Chinese warplanes and six naval vessels operating around Taiwan during the 24-hour period leading up to 6:00 am (2200 GMT).
A second statement said a further 26 aircraft were detected after that time.
The ministry added it had "monitored the situation and responded accordingly".
The latest incursions came after the Chinese coast guard seized a Taiwanese boat over suspected illegal fishing off the coast of China's Quanzhou and close to Taiwan's offshore Kinmen islands.
Taipei insisted that the boat was operating in a "traditional fishing ground" for both sides and demanded its immediate release.
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