There have been two other fatal accidents and another two major incidents in the airline's history, according to data from Flightglobal Ascend, an industry consultancy.
In December 2012, an ATR 72-200 freighter crashed en route to Macau from Taipei, killing both crew members. In 1995, an ATR 72-200 crashed into a hill near Songshan, killing all four crew.
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In 2003, an Airbus A321 was written off after colliding with a vehicle that had strayed onto the runway while the plane was landing. A year later, an Airbus A320 was severely damaged when it over-ran the runway while landing at Songshan.
There were no fatalities in either of those incidents.
Investigators into the latest disaster are likely to focus on cockpit procedures and maintenance issues at the airline, said Greg Waldron, Asia Managing Editor at Flightglobal.
"Coming so soon after July's crash, the airline could come under intense scrutiny by regulators, not to mention the impact this will have on public perceptions of the carrier," he added.
TransAsia chief executive Chen Xinde bowed at a news conference, carried live on Taiwan television, as he offered a "deep apology" for the accident. The company, whose share price dropped 7 percent on Wednesday, was not answering calls for comment.
The Civil Aeronautics Administration said it would not make further comment until an investigation into the crash was completed.
Taiwan had a poor air safety record from the 1980s to the early 2000s due to several fatal crashes, mostly at flag carrier China Airlines.
Before last year's TransAsia incident, Taiwan's last fatal crash came in May 2002 when a China Airlines Boeing 747-200 broke up mid-air on the way to Hong Kong, killing all 225 people on board.
That prompted the Taiwan government, with help from agencies such as the International Air Transport Association (IATA), to revamp its regulatory agencies.
China Airlines also reviewed its procedures and passed IATA's International Operational Safety Audit (IOSA) in 2005, which meant that it met global safety standards.
The focus now is on TransAsia, which was listed on the Taiwan stock exchange in November 2011 and remains a much smaller player than China Airlines and EVA Air.
The airline, which also has Airbus A320s and A330s, mainly operates services from Taiwan to other Northeast Asian destinations in China and Japan. It also has services to South Korea, Macau, Thailand and Cambodia.
Its ambitious management has, in the past, expressed hopes of eventually becoming a larger carrier with services to Europe or the United States using aircraft such as the Airbus A380.