The latest sorties came a day after China flew 103 warplanes in the 24-hour window from Sunday to Monday morning around Taiwan, which the island's authorities said was a "recent high" number.
On Tuesday, the ministry said China flew 55 aircraft and sailed seven naval vessels around the island from Monday to Tuesday morning.
Beijing claims Taiwan as its own territory to be seized one day, and has ramped up diplomatic and military pressure on Taipei in recent years.
On Tuesday, Taiwan's ministry accused China of carrying out "provocative actions" that were leading to "rising tensions and deteriorating regional security."
Around half of the 55 warplanes detected crossed the so-called median line of the Taiwan Strait that separates the island from China, and entered its southwest and southeast air defence identification zone (ADIZ), Taipei said.
On Monday, Taiwan had urged China to "immediately stop such destructive unilateral actions."
China's foreign ministry did not comment on the sorties on Monday, though its spokeswoman Mao Ning reaffirmed Beijing's position that Taiwan belongs to China.
She also reiterated Beijing's policy that "the so-called median line does not exist".
Taipei has reported a marked uptick in the number of incursions by Chinese warplanes and ships in recent days.
Beijing said last week its troops were on "high alert" after two ships belonging to the United States and Canada sailed through the Taiwan Strait.
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