The ATR 72 turboprop aircraft crashed at at a village named Xixi which is very near to Magong Airport after its failed attempts of emergency landing.
The domestic TransAsia Airways plane departed from the southern municipality of Kaohsiun at 0943 GMT (1743 local time) but contact with the control was lost at 1906, CNA said citing the Civil Aeronautics Administration.
The aircraft caught fire just after it crashed, the report said.
A total of 54 passengers and 4 crews were on board at the time of crash, Taiwans CNA news agency reported.
“It was thunderstorm condition during the crash”, a fire department offical said. Earlier on Wednesday, Taiwan was hit by a Typhoon name Matmo by its strong winds and rain.