The single-seat Mirage-2000 flown by Captain Ho Tzu-yu disappeared from radar off the northeast coast of the island, 34 minutes after takeoff on Tuesday.
Seventeen military planes as well as 10 naval and coastguard vessels were dispatched to conduct a search, but there has so far been no sighting of the missing plane.
"We hope Ho can be safely rescued soon," said Lieutenant General Chang Che-ping, the air force's deputy chief.
All Mirage jets have been grounded since the incident.
Chang described Ho, 28, as an "excellent pilot," and that there were no signs of any problems or irregularities after he took off from a base near the city of Hsinchu.
Ho graduated from the Air Force Academy in 2013, and had accumulated about 227 hours in the Mirage-2000.
Chang declined to comment on reports Ho's health may have been a factor in the disappearance, saying an investigation into the cause of the incident was still under way.
The air force confirmed Ho took time off work last year on health grounds, but declined to elaborate.
Taiwan purchased 60 Mirage 2000-5 jets in 1992 from France in an arms deal that upset China.
Beijing claims sovereignty over Taiwan, even though the two sides split in 1949 after a civil war, and is fiercely opposed to the island developing its own military capability.
There were four accidents involving Mirage fighters in Taiwan between 1999 and 2013, killing three pilots. In 2012, Taiwan temporarily grounded all its Mirage jets after a pilot died while conducting a training mission in France.