Taiwan's Civil Aeronautics Administration (CAA) ordered all the airline's staff who fly ATR planes to take tests on operating the aircraft after it emerged the pilots may have inexplicably shut off one of the engines before Flight GE235
went down last week.
"Starting today, all of TransAsia's 71 ATR pilots will undergo tests to be carried out by the CAA and third-party professional units for an estimated period of four days," the carrier said in a statement.
"As a result, some of our domestic flights will be adjusted," it said, explaining that 90 domestic flights will be cancelled by Monday.
Pilots who fail the tests will be grounded immediately for an indefinite period of time pending further qualification training, according to the CAA.
On Wednesday, a TransAsia ATR 72-600 plane plunged into a river in Taipei with 53 passengers and five crew members on board. Thirty-nine people were killed, fifteen survived and rescuers are still searching for another four who remain missing.
The bodies of one man and two women, as yet unidentified, were found downstream of the crash site during a blanket search of the river by hundreds of rescuers and divers, Taipei city fire department said on Saturday.
A fourth woman, wearing flight attendant's uniform, was located in the river in the afternoon.
The latest accident comes after aviation authorities said TransAsia Airways had failed to meet around a third of the regulatory requirements imposed after another fatal crash in Taiwan's western Penghu islands in July.
Investigators are still trying to establish what caused Wednesday's crash, but initial reports from the planes black boxes found the right engine had "flamed out" about two minutes after take-off.
Warning signals blared in the cockpit and the left engine was then shut down manually by the crew for unknown reasons, Taiwan's Aviation Safety Council said.
"The pilot tried to restart the engines but to no avail. That means that during the flight's final moments, neither engine had any thrust," said the council's director Thomas Wang. "We heard 'Mayday' at 10:54:35."
Analysts have said the pilots may have caused the crash by turning off the wrong engine.

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