The pilot is believed to have ejected from his single-seat F-16V off Taiwan's east coast on Tuesday around 70 minutes after taking off for a routine training mission, according to the Air Force.
Thirty aircraft, 22 naval and coast guard vessels, and two drones have been deployed to check the waters, while a ground search is also underway, Defence Minister Wellington Koo said.
"Our only goal right now is to do everything we can to conduct the search and rescue operation," Koo told reporters in the parliamentary compound.
Koo said combat exercise and training missions have been suspended for the inspection of F-16s, but "alert and standby duties will be maintained."
"This inspection should be completed by Saturday. This will not create any gaps in air defences," he said.
Taiwan is upgrading its defence capabilities as China maintains military pressure on the democratic island, which Beijing claims is part of its territory.
The island has ordered 66 US F-16V -- a fourth-generation multi-role fighter -- that is a significantly upgraded version of Taiwan's ageing F-16 A/B jets.
Taiwan completed upgrades of 141 older F-16s to the V standard in late 2023.
The aircraft were due to be delivered in 2026, but Koo said recently that would be "challenging".
Koo told lawmakers on Thursday that 56 aircraft have already been assembled on the production line, but he did not reply when asked how many could be delivered in the first half of this year.
China has in recent years ramped up incursions by fighter jets and warships around Taiwan -- actions that military experts dub as grey-zone tactics that serve to exhaust the island's armed forces.
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