The ministry earlier this month, in a strongly worded statement, accused China of threatening aviation safety and waging psychological warfare on the island's people with the balloons, days before Taiwan's Jan. 13 elections.
China's defence ministry, which last month declined to comment on the balloons, did not immediately respond to a request for comment. China claims Taiwan as its own territory, despite the strong objections of the government in Taipei.
The potential for China to use balloons for spying became a global issue last February when the United States shot down what it said was a Chinese surveillance balloon. China said the balloon was a civilian craft that accidentally drifted astray.
In the latest incident, revealed by the ministry on Monday in its daily report on Chinese military activities over the past 24 hours, it said six balloons had flown over the strait's sensitive median line on Sunday.
However, only one crossed Taiwan island, at its southern tip, according to a map the ministry provided.
The other five balloons flew to the north of Taiwan but did not fly over land, the ministry said.
The balloons all headed east before vanishing, it added.
The Taiwan Strait's median line previously served as an unofficial barrier between Taiwan and China, but Chinese fighter jets, drones and now balloons regularly fly over it.
