TAIPEI—Rescuers worked through the night to recover bodies and wreckage from TransAsia Airways Flight 235 after it crashed Wednesday morning, clipping a highway overpass before slamming into a river just four minutes after taking off.

At least 31 of the 58 people on board were killed, Taiwan’s Civil Aeronautics Administration said. TransAsia said the two pilots and a pilot-in-training were among the dead. Twelve were still missing early Thursday, and 15 survived with injuries. It was TransAsia’s second deadly crash in seven months. (Read more: Rescuers race to recover bodies, wreckage.)

The cause of the crash wasn’t known.

The control tower lost communication with the pilots four minutes after takeoff from Taipei’s Songshan Airport, officials said. The plane was en route to Kinmen, a Taiwanese island near China’s mainland, around 10:53 a.m. local time. Many of the passengers were mainland Chinese tourists.

Air-safety concerns in Asia have been growing as the region’s traffic continues to boom and in response to a series of tragedies last year, including the Dec. 28 crash of AirAsia Flight 8501, which went down in the Java Sea after taking off from Surabaya, Indonesia, on its way to Singapore. The exact cause of that accident is unclear. Memories of Malaysia Airlines Flight 370, which disappeared nearly a year ago and still hasn’t been found, also haunt the region.