As the rescue operation continued into the night, a crane lifted the rear and central sections of the plane from the water, with one body retrieved from inside.
The front part, where 17 people are believed to be trapped, was still in the water.
TransAsia said 16 survivors had been pulled out of the wreckage after the turboprop plane crashed with 58 people onboard. Many of the passengers were mainland Chinese tourists.
Cold weather, poor visibility and rising water levels were hampering the rescue, officials said, admitting they were now "not optimistic" about finding survivors.
Dramatic amateur video footage showed the TransAsia ATR 72-600 hit an elevated road as it banked sidelong towards the Keelung River, leaving a trail of debris including a smashed taxi.