The balloons were spotted along with five Chinese aircraft and six warships in the 24 hours to 6:00 am (2200 GMT on Thursday), the ministry said in its daily report.
It was the highest number of balloons recorded, said the ministry, which started regularly releasing the data on balloon sightings since December 2023.
"Based on trajectory analysis, most balloons around the Taiwan Strait are used for meteorological sounding purposes," it said in a statement.
"Large-scale, planned and intensive deployment (of balloons) has caused potential harm to flight safety".
China insists self-ruled Taiwan is part of its territory and has threatened to use force to bring the island under its control.
Beijing has increased the deployment of fighter jets and naval vessels around Taiwan in recent years to press its claim of sovereignty, which Taipei rejects.
The surge in balloons comes after Taiwan recorded 45 Chinese aircraft near the island in a 24-hour period last week, which was the highest number this year.
In the same week, Taipei also condemned China for holding "live-fire" drills off the island's south.
Beijing hit back, accusing Taiwan of "pure hype" over what it called "routine training".
The top US military commander in the Indo-Pacific told a defence forum last month that the frequency of China's exercises could be used to cover up a real attack.
In response to those comments, China's defence ministry reiterated that Beijing would not renounce the use of force to achieve unification.
Taiwan is a potential flashpoint for a war between China and the United States, which is the island's most important backer and biggest arms supplier.
While the United States is legally bound to provide arms to Taiwan -- which Beijing opposes -- Washington has long maintained "strategic ambiguity" when it comes to whether it would deploy its military to defend it from a Chinese attack.
Despite long-standing strong bipartisan support in the US Congress for Taiwan, there are fears that US President Donald Trump might not consider the island worth defending if China attacked.
Speaking at a recent security forum, Taiwan's National Security Council chief Joseph Wu said US support for Taiwan was "very strong".
Wu praised the United States for providing defence equipment to Taiwan, training its soldiers and boosting its international presence.
"I think the Trump administration's support for Taiwan will remain very strong," Wu told the HFX Taipei Forum.
"I think it's very clear that the United States is supporting Taiwan, and with the US support, I think we will be more confident in defending ourselves."
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