The domestic TransAsia Airways flight crashed and caught fire near Magong airport on the outlying Penghu island,
News agency CNA reported that there were 54 passengers and four crew on board flight GE222 at the time of the incident.
Aviation officials later revealed that the pilot had aborted an initial attempt at landing before the crash.
Transport minister Yeh Kuang-Shih said 47 people had been killed and 11 survivors were being treated for their injuries.
One local news report claimed a fire brigade chief had said 51 people had been killed in the incident. Civil aviation director Jean Shen reportedly said: “The scene of the crash is chaotic.”
Firefighters and other emergency personnel were at the scene last night, using torches to search for survivors and recover bodies.
Firefighters were seen examining the debris, shining lights to illuminate the wreckage in the darkness.
The plane left the southern municipality of Kaohsiung at 5:43pm local time (9:43am GMT), but lost contact with air traffic controllers at 7:06pm local time, CNA said, citing the Civil Aviation Authority.
The plane crashed in flames near Xixi village while attempting to land in stormy weather.
Flight GE222, an ATR-72 aircraft operated by Taiwanese airline TransAsia Airways, was heading from the southern port city of Kaohsiung to Penghu, an island halfway between the Chinese mainland and Taiwan in the Taiwan Strait.
Taiwan had been battered by Typhoon Matmo and forecasters warned of heavy rain yesterday evening, as the eye of the storm moved over mainland China.
Taiwan’s weather agency said Typhoon Matmo had gusts of 67 miles an hour and was moving at 12mph. The Fujian province’s flood control headquarters said nearly 300,000 people had been evacuated ahead of the storm.
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.
David Vargas, a spokesman for plane manufacturer ATR, said: “We are aware of the crash. We are trying to get more information and confirm what went wrong.”