The failed pilots will undergo retraining before being allowed to fly again, the airline said, adding that each had an average of 6,900 flying hours, not a insignificant number for a commercial pilot.
The 39 pilots who passed the oral test will have to sit a simulator test — if they don't pass, they too will be grounded, TransAsia said.
Nineteen other pilots have yet to take any of the tests, but they won't be assigned any duties until they do so.
The testing was recommended by Taiwan's Civil Aeronautics Administration for pilots at the controls of ATR turboprop aircraft, the type involved in the February 4 crash.
Search for bodies
Meanwhile, rescue workers continue to search the muddy depths of the Keelung River in Taipei, where the flight went down, for the last unaccounted passenger.
Two bodies were found around 600 meters downriver from the crash site on Tuesday, taking the final death toll to 42.
Officials said the bodies found were still strapped in their seats.
Fifty-one search boats, three helicopters, and more than 450 people are working to find the remaining passenger, according to a statement from the Taipei City mayor's office.
Excavators are being used to dig the river bed amid theories that the final victim may be stuck in mud.
Crash caught on camera
TransAsia Flight GE235 crashed minutes after takeoff in the Taiwanese capital after the pilots struggled to correct problems with both engines, according to preliminary investigations by Taiwan's Aviation Safety Council.
The agency said the aircraft's engines stopped producing power, one after the other, leaving the plane flying without thrust for more than one minute.
Dashcam video taken by cars on a nearby highway showed the plane turning sharply left, before the wing hit the overpass and crashed into the river.
Fifteen people survived the crash after being pulled from the submerged wreck.
After the crash, Taiwan's aviation authorities ordered special checks on all ATR 72s in the fleets of local carriers.
TransAsia was involved in another deadly disaster last July. Forty-eight people died after an ATR 72 aircraft crashed as it was attempting to land in the Taiwanese Penghu Islands during bad weather.