Data from the “black box” flight recorders retrieved from the wreckage suggests the pilots shut down one engine after the other lost power.
Earlier, TransAsia said all of its pilots would be retaking proficiency examinations following the disaster.
Fifteen of the 58 people on board were rescued but at least 35 others died.
Thomas Wang, executive director of Taiwan’s Aviation Safety Council, said the plane’s right engine triggered an alarm just 37 seconds after taking off from the Taipei’s Songshan airport.
The main pilot could be heard on black-box recordings saying the engine had experienced a “flame-out”, Mr Wang said, which can occur when the fuel supply to the engine is interrupted.
However, he said data showed that the engine had in fact been moved into idle mode.
Seconds later, the pilots shut down the left engine, meaning neither engine was producing any power. A restart was attempted, but the plane crashed 72 seconds later.
Officials said it was unclear why the left engine had been turned off, especially as the plane, an ATR 72-600, is able to fly with just one functioning engine.
Mr Wang said it was too early to draw firm conclusions about why the first engine had lost power but he told the BBC that the pilots had followed normal procedure.
“It’s only the third day so we can’t say too much,” he said. “We haven’t ruled anything out.”
The flight, which had been bound for Taiwan’s Kinmen Island, crashed into the Keelung River.
A more substantial report into the crash is expected to be released within the next 30 days, ahead of the publication of a final report in the next three to six months.
Earlier, Taipei’s mayor praised the main pilot, Liao Chien-tsung, for steering the plane away from blocks of flats and commercial buildings before it came down.
Taiwanese Vice-President Wu Den-yih also paid tribute to the 42-year-old pilot, saying he had “meticulously grasped” the flight controls in the plane’s last few seconds.
“In the final moments he still wanted to control the plane to avoid harming residents in the housing communities,” Mr Wu told reporters.
Crash investigators told Taiwanese media that Mr Liao’s hands were still on the plane’s controls when his body was found.
Both the pilot and co-pilot were found dead in the cockpit, according to local media reports.
Taiwan’s aviation regulator has ordered thorough engine and fuel system checks on the remaining 22 ATR-manufactured aircraft currently in active service on the island.
The BBC’s Cindy Sui in Taipei said search-and-rescue teams had been focusing their efforts downstream of the crash site, and are carrying out operations along a 15-km (9-mile) stretch of the river.
The main parts of the plane, which had been submerged, have been retrieved from the water.
Divers are now attempting to locate the remaining victims and four more bodies were retrieved from the water on Friday.