The single-seat jet disappeared off the radar over mountainous terrain in the northeastern county of Keelung at 13:43 pm (0543 GMT), 34 minutes after take off, the air force said.

The defence ministry, local police and fire department had conducted land and air searches for the 31-year-old pilot, Major Wu Yen-ting, for hours before discovering the wreckage of the plane on Monday evening.

"It is confirmed that the pilot has died in the line of duty ... a commission will be set up later to investigate and clarify the cause of the incident," the air force said in a statement.

President Tsai Ing-wen and Defence Minister Yen De-fa expressed their condolences and pledged compensation to the pilot's family.

Wu was also involved in the last F-16 accident in Taiwan, in 2013, when he parachuted to safety following a suspected mechanical failure.

The five-day "Han Guang" (Han Glory) drill kicked off Monday with troops practising thwarting a Chinese "invasion" by simulating surprise coastal assaults to reflect increased military threats from Beijing.

Although Taiwan is a self-ruling democracy, it has never formally declared independence from the mainland and Beijing still sees it as a renegade province to be brought back into the fold, by force if necessary.

Taiwan's defence ministry has said the main goal of the drill is to counter any future Chinese military mission to the island.

As relations have soured between Beijing and Taiwan's President Tsai Ing-wen, China has increasingly flexed its military muscles.

It held live-fire drills in April in the Taiwan Strait -- the narrow waterway separating the Chinese mainland from Taiwan -- following weeks of naval manoeuvres in the area.

In November, Taiwan's air force temporarily grounded all its Mirage jets as it searched for a pilot who went missing while conducting a training mission in one of the French-made fighters. Both pilot and plane are yet to be found.