The domestic TransAsia Airways flight crashed near Magong airport on the outlying Penghu island, reports said.
There were a total of 54 passengers and four crew on board, Taiwan's CNA news agency reported.
Aviation officials said flight GE222 aborted its initial landing and then crashed, local media reported.
Transport minister Yeh Kuang-Shih said that 47 people were killed and 11 were injured, CNA reported.
The agency previously said that 51 were feared killed, citing fire department officials.
"It's chaotic [at] the scene," Jean Shen, director of the Civil Aeronautics Administration, told Reuters news agency.
'Plane in flames'
Firefighters and other emergency personnel are attempting to rescue those on board.