One of the two engines on TransAsia Airways Flight 235 went idle 37 seconds after takeoff, and the pilots apparently shut off the other before making a futile attempt to restart it.
It was unclear why the second engine was shut down, since the plane was capable of flying with one engine.
Taiwan's official China News Agency said investigators were looking into the possibility of "professional error".
Wednesday's crash into a river in Taipei minutes after takeoff killed at least 36 people and left seven missing.
Fifteen people were rescued with injuries after the accident, which was captured in a dramatic dashboard camera video that showed the ATR 72 propjet banking steeply and scraping a highway overpass before it hurtled into the Keelung River.
There would be no reason to have shut down the good engine, experts said.
The details on the engines were presented at a news conference in Taipei by aviation safety council executive director Thomas Wang as preliminary findings from the flight data recorder.
He said the plane's right engine triggered an alarm 37 seconds after takeoff.
However, he said the data showed it had not shut down, or "flamed out" as the pilot told the control tower, but rather moved into idle mode, with no change in the oil pressure.
Then, 46 seconds later, the left engine was shut down, apparently by one of the pilots, so that neither engine was producing any power. A restart was attempted, but the plane crashed just 72 seconds later.
TransAsia said all 71 of its ATR pilots would retake proficiency examinations as requested by the Civil Aeronautics Administration.
The pilot had 4,900 hours of flying experience, said Lin Chih-ming of the civil aeronautics administration.
Taiwanese vice president Wu Den-yih, mindful of the island's reputation as a tourist destination and its tense relations with China where most of the flight's passengers were from, went to a Taipei funeral parlour for prayer sessions to pay respects.
He expressed condolences and praised pilot Liao Chien-chung, who died in the crash. The pilots may have deliberately steered the plane away from buildings and into the river in the final moments.
"When it came to when it was clear his life would end, (the pilot) meticulously grasped the flight operating system and in the final moments he still wanted to control the plane to avoid harming residents in the housing communities," Mr Wu said.
Divers with a local fire agency found one female and three male bodies yesterday along the muddy Keelung River bottom about 50 yards from the crash site.
The agency suspects the eight bodies that are still missing may be in equally murky areas and has sent 190 divers to look for them.
Taiwan's ministry of national defence dispatched three S-70C rescue helicopters to search along a river system that runs into the ocean off Taiwan's north-west coast.
More than 30 relatives of victims cried wildly, prayed or were comforted by Buddhist volunteers at the riverside crash site as divers in black wetsuits brought back the four bodies.
The pilot's and co-pilot's bodies were found earlier with their hands still on the controls, Taiwan's ETToday online news service said.
Evidence the TransAsia pilots may have shut down the wrong engine drew comparisons with the 1989 crash of a British Midland Airways Boeing 737 jet after takeoff from London's Heathrow Airport.
In that accident, a fan blade failure in the left engine led to vibrations and smoke and fumes in the cockpit.
The pilots believed that the right engine had failed and reduced power to it, which caused the vibrations to stop, convincing the crew that they had identified the troubled engine.
As the pilots tried to make an emergency landing at East Midlands Airport, the left engine quit, and attempts to restart the right engine failed.
The plane crashed half-a-mile short of the runway, killing 47 people, while 79 survived.