TransAsia will pay funeral subsidy worth 800,000 new Taiwan dollars (around $26,600) to each family of the victims, and 27 families have been compensated, Xinhua quoted the aviation safety council as saying.
The flight carried 54 passengers, including two French nationals, and four crew members.
Ten people survived the crash with injuries, but 48 have been confirmed dead.
Taiwan's civil aeronautics authority said in an announcement that the accident may have been caused by compound reasons, including weather condition, machinery fault and human factor.
The civil aeronautics authority and TransAsia will provide all gathered information to the aviation safety council to help in the investigation, the announcement said.
The domestic plane was going from Kaohsiung in southern Taiwan to Penghu Islands in the west.
The flight, which took off from Kaohsiung on Wednesday evening, crashed into residential buildings in Xixi Village of Penghu, Taiwan's western island, after a failed emergency landing at Magong airport.