The two F-5E fighter jets disappeared from radar around 3 pm (0700 GMT) some 2.6 kilometers off the coast of rural southern Pingtung county, Taiwan’s National Rescue Command Centre said.
An air force helicopter, coast guard, and other rescue ships are looking for the missing pilot, it added.
The F-5E is an older generation fighter with a design that dates back to 1965.
Taiwan was the largest operator of the type at one time, having 336 F-5E/Fs in inventory.