The balloons were seen crossing the median line over the Taiwan Strait -- a sensitive waterway separating the island from China -- late January 1 at two locations, one near the western city of Chiayi and another by Keelung in the north.
An accompanying graphic released by the ministry showed one balloon headed east directly above the island after appearing northwest of Chiayi on the western coast.
They were at "the altitude of approximately 30,000 and 32,000 feet (9-10 kilometres)," it said in a statement.
"The balloons headed northeast and disappeared at 23:43 yesterday and 00:43 today."
The sightings of Chinese balloons began last month as the island's pivotal presidential election on January 13 approaches.
Taiwanese authorities have so far reported six incidents in December.
Chinese balloons became a politically fraught topic in February when the United States shot down what it called a spy balloon over its territory, with Beijing saying the craft was a civilian airship blown off course.
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