"1 PRC (People's Republic of China) balloon was detected at 11:52 (0352 GMT) yesterday after crossing the median line of the Taiwan Strait ... 101 nautical miles (187 kilometres) southwest of Keelung," said the ministry, referring to a city in northern Taiwan.
"The balloon headed east and disappeared at 12:55 (0455 GMT)," it added.
The ministry included a graphic showing the balloon on a meandering path.
"Our preliminary understanding is that it might be a sounding or a weather balloon that drifted toward Taiwan due to monsoon winds," Defence Minister Chiu Kuo-cheng told reporters Friday.
He added that such a balloon could be used for gathering meteorological research and data, like the impact of wind forces.
On Thursday, the ministry reported it had detected seven Chinese aircraft crossing the median line at 7:30 pm.
"The aircraft also conducted joint combat patrol with (Chinese) vessels," it said, adding that it had monitored and tasked "land-based missile systems to respond".
A Friday morning report said 27 planes had crossed the line in a 24-hour window ending at 6 am.
China has in recent years ramped up military and political pressures on democratic Taiwan, which it claims as its territory.
While Beijing has been sending warplanes and vessels around Taiwan on a near-daily basis, nighttime activity by Chinese aircraft and the appearance of a balloon are rare.
Defence analyst Su Tzu-yun said there have been past instances of small Chinese weather balloons floating above Taiwan's main island and smaller outlying areas, which "do not pose a military threat".
But Thursday's balloon "could be a deliberate test", Su, who is with Taiwan's Institute for National Defence and Security Research, told AFP.
"Besides meteorological purposes, it could also be a deliberate test conducted by the (China's) Eastern Theater Command or a political signal," he said, adding that they could be a form of "political harassment".
China's foreign ministry spokesman Wang Wenbin said he was "not aware" of the situation.
In February, a Chinese spy balloon that flew across the United States was shot down by a US fighter jet, causing a diplomatic furor.
The huge balloon, which carried a large payload of electronics, flew over sensitive US military installations and prompted concerns Beijing was scooping up vital intelligence.
A US official said at the time the balloon had multiple antennas including an array likely capable of collecting and geo-locating communications.
China denied that the balloon was to collect intelligence and said it had strayed off course in entering US airspace.
The Pentagon concluded in June that the balloon did not gather data.
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