TransAsia Airways on Saturday started the first day of a programme to retrain its pilots after its second deadly crash in seven months, as rescuers retrieved three more bodies from the drowned plane.

Taiwan's Civil Aeronautics Administration (CAA) ordered all of TransAsia's 71 pilots who fly ATR planes to take oral tests on operating the aircraft as part of the retraining, after it emerged the pilots may have inexplicably shut down one of the engines before the crash.

"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 airline 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.

On Wednesday an ATR 72-600 plane plunged into a river in Taipei on Wednesday with 53 passengers and five crew members on board. 38 people were killed, fifteen survived and rescuers are still searching the river and submerged wreckage for another five 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, Taipei city fire department said.

Aviation authorities said TransAsia Airways had failed to meet around a third of the regulatory requirements imposed after another fatal crash seven months ago in Taiwan's western Penghu islands.

Investigators are still trying to establish what caused Flight GE235 to crash, but initial reports from the planes black boxes found the right engine had "flamed out" about two minutes after taking off from an airport in northern Taipei.

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 Friday.

The chief pilot of has been hailed as a hero after reports emerged his body was found still clutching the joystick, after he apparently battled to avoid populated areas.

TransAsia has announced that it will invite international aviation safety experts to conduct a year-long safety review of the company as well as adopting measures to enhance its organisation and training as well as adjusting existing routes.