The ministry said the balloons were spotted on Saturday, the first day of the Lunar New Year holiday, at an altitude of 12,000 to 35,000 feet.
Five of the balloons flew directly over the island, and one grazed its northern tip, according to a map released by the ministry.
China claims democratic Taiwan as its own territory and has not 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, with balloons also increasingly flying over the island.
A batch of eight balloons were also detected on Friday, the highest number since the defence ministry started regularly releasing data on balloon sightings in December.
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.
It did not, however, send a major contingent 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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