Five were seen near the northern coastal city of Keelung while one flew above the island near southern Pingtung county, a map released by the ministry showed.
The defence ministry, which releases daily data on China's military presence around Taiwan, said the balloons were all spotted on Sunday at an altitude from 15,000 feet to 17,000 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.
It has ramped up military pressure in recent years and deployed warplanes and naval vessels around the island on a nearly daily basis.
Last February, 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 this 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 Lai's win 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.
The largest incursion since the election was last Thursday when 24 Chinese warplanes were detected around Taiwan, with 11 crossing a sensitive median line separating the island from China, according to Taipei.
But Beijing drew first blood in the political sphere, with Pacific nation Nauru abruptly switching diplomatic recognition from Taiwan to China last week, leaving Taipei with 12 official allies.
The largest number of warplanes China has sent during a 24-hour window came in September, when Taiwan detected 103 Chinese aircraft around the island.
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