The ministry said the balloons were spotted on Friday, the day before the start of the Lunar New Year holiday, at an altitude of 15,000 feet (4,572 metres) to 38,000 feet.
It was the highest number detected since the ministry started regularly releasing data on balloon sightings in December.
China claims democratic Taiwan as its own territory and has never renounced the use of force to bring the self-ruled island under its control.
Beijing has ramped up military pressure in recent years, and deploys warplanes and naval vessels around the island on a nearly daily basis.
In February last year, Taiwan's military alerted aviation authorities after spotting a balloon floating in the island's airspace but did not say where the balloon came from or provide a detailed location.
The latest balloon sightings came after Taiwan's presidential election last month, which was won by the ruling Democratic Progressive Party's Lai Ching-te, who Beijing regards as a "separatist".
China warned ahead of the vote that a win by Lai would bring "war and decline" to Taiwan.
But it did not send an oversized number of warplanes and naval vessels in the election's immediate aftermath.
Since the January 13 vote, the largest incursions included 33 Chinese warplanes detected around Taiwan, according to Taipei.
The largest number of warplanes China has sent during a 24-hour window came in September, when Taiwan recorded 103 Chinese aircraft around the island.
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