Maj Wang Ching-chun and 1st Lt Huang Chun-jung were piloting the AT-3 Air Force Academy training craft when it lost contact with air traffic controllers on Tuesday, the news agency said.
Taiwan's Ministry of National Defense said authorities found aircraft debris and confirmed it to be from the missing plane in the early hours of Saturday.
The pilots did not issue any abnormal calls before they lost contact and the aircraft's flight record in the past three months showed no irregularities, the news agency said. The cause of the crash was under investigation, it said.