China and Taiwan have been ruled separately since 1949, but Beijing considers it part of its territory and has refused to renounce the use of force to bring the island under its control.
Beijing regularly deploys fighter jets, drones and warships, and occasionally balloons, around Taiwan as it keeps up military pressure.
Thursday's early morning exercise was aimed at testing "the response and engagement procedures of air defence units", Taiwan's Air Force Command said in a statement.
"Various types of aircraft, ships, and air defence missile systems were deployed from 5:00 am to 7:00 am," the statement said, without providing details.
The last time the Air Force Command held the Integrated Air and Missile Defence Exercise was in June, a month after Taiwan President Lai Ching-te took office.
Lai, who has been outspoken in his defence of Taiwan's sovereignty, is due to leave Saturday for a trip to three Pacific island nations, with a likely stopover on US soil.
The trip is aimed at shoring up Taiwan's dwindling number of diplomatic allies and is likely to elicit an angry response from China, which opposes any attempt to give Taipei international legitimacy.
Taiwan's defence ministry also reported Thursday that it had detected two Chinese balloons over waters north of the island.
The balloons were spotted Wednesday afternoon in two locations about 111 kilometres (69 miles) northwest and 163 kilometres north of Keelung City.
That follows the sighting of a Chinese balloon on Sunday over the same waters.
Along with the two balloons, 13 Chinese military aircraft and seven navy vessels were spotted around Taiwan in the 24 hours to 6:00 am on Thursday, the ministry said.
Taiwan lives under the constant threat of a Chinese invasion and has ramped up defence spending in recent years to strengthen its military capabilities.
The island has a home-grown defence industry but also relies heavily on arms sales from Washington, which is Taiwan's most important partner and biggest provider of weapons and ammunition.
Taiwan has described the balloons as a form of "grey zone" harassment -- a tactic that falls short of an act of war.
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