A graphic released by the ministry showed three balloons headed northeast above Taiwan after appearing "southwest of Ching-Chuan-Kang", home to a military airbase in the western city of Taichung.
The lowest altitude measured for one of them was 12,000 feet (3,658 metres).
Tuesday's balloon incidents came less than two weeks before the self-ruled island will hold a pivotal election and was the second consecutive day such objects were detected above Taiwan.
The ministry began reporting them for the first time in December, publicly identifying six incidents.
It said Wednesday it was "closely monitoring and will take appropriate measures" on the balloons, depending on the "nature, altitude and possible hazards of the targets".
Conflict expert Ou Sifu of Taiwan's Institute of National Defense and Security Research said the balloons are "for military coercion and psychological warfare".
"The presidential election is coming and balloons are a kind of military intimidating tool," he told AFP, adding that China wished to influence more "pro-Beijing votes".
Beijing claims Taiwan as part of its territory and has in recent years ramped up military and political pressures against the government of President Tsai Ing-wen.
It has sent in unprecedented numbers of warplanes and naval vessels around the island, dubbed by conflict experts as "grey zone" tactics that serve to intimidate Taiwan's military.
Beijing has also refused to engage with Tsai during her tenure, as she does not acknowledge China's claim on Taiwan.
Her deputy Lai Ching-te -- a self-proclaimed "pragmatic worker for Taiwan's independence" -- is the current frontrunner for the January 13 election.
Beijing has dubbed him a "troublemaker" and a "separatist".
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