The plane, a 70-seat turboprop ATR 72, crashed near the runway with 54 passengers and four crew on board, it said.
"It’s chaotic on the scene," CAA director Jean Shen told Reuters.
Eleven injured people had been taken to hospital, the government said.
Authorities said TransAsia Airways flight GE222 crashed near Magong airport on one of the outlying Penghu islands, also known as the Pescadores, after having requested a second attempt to land.
Television images showed firefighters working at site of the mangled wreckage and soldiers on the scene.
There were conflicting reports of the death toll from officials and local media.
"Fifty-one people are feared dead and seven people injured," the Civil Aeronautics Administration's Shen Chi initially told reporters.
The island's local fire chief put the death toll at 45 while media reports said 47 were killed.
"The control tower lost contact with the aircraft soon after they requested a go-around (second attempt to land)," Shen told reporters.
It was flying from Kaohsiung and had been delayed due to bad weather, according to Shen.
Typhoon Matmo slammed into Taiwan on Wednesday with heavy rains and strong winds, shutting financial markets and schools, and leaving at least nine people injured.
TransAsia Airways is a Taiwan-based airline with a fleet of around 23 Airbus and ATR aircraft, flying chiefly on domestic routes, but with some flights to Japan, Thailand and Cambodia among its Asian destinations.
Apart from Wednesday's event, Taiwan's aviation safety council says TransAsia has had a total of 8 incidents since 2002, including 6 involving the ATR 72.
source: interaksyon.com
