He assured reporters that it was a satellite, explaining that the alert was issued because of possible “debris”.
“When a rocket is openly flying in our sky, some of their tubes or debris will fall in this region,” Wu told reporters.
“That’s the reason why our national alert centre will issue this kind of alert. It has happened before.”
Saturday’s election will be closely watched from Beijing to Washington as voters choose a new leader to steer the island in the face of an increasingly assertive Beijing.
Front-runner Lai Ching-te, Taiwan’s current vice president, accused Beijing of using “all means” to influence Saturday’s vote.
China has maintained a near-daily military presence around Taiwan, sending in fighter jets, naval vessels and drones.
The latest incursion came on Monday when four balloons flew over the island, according to Taiwan’s defence ministry, while 10 Chinese warplanes and four naval vessels were also observed.
China’s state-run Xinhua news agency said the satellite will be used to make astronomical observations, in particular “mysterious transient phenomena in the universe comparable to the flickering of fireworks”.