Taiwanese officials Thursday defended flight clearance given to a plane which crashed while trying to land during stormy weather, killing 48 people, as sobbing relatives gathered to identify their loved ones.

Flight GE222 was carrying 54 passengers and four crew members on a domestic flight when it crashed on Wednesday at Magong on the Penghu island chain, with ten surviving the disaster.

Two French medical students were among the dead, the foreign ministry in Paris said.

The ATR 72-500 was flying from the southwestern city of Kaohsiung to the islands off the west coast and had been delayed by bad weather as Typhoon Matmo pounded Taiwan, according to authorities.

It was trying to land for a second time after aborting the first attempt during thunder and heavy rain, crashing into two houses near Magong airport and injuring five people on the ground, officials said.

Questions have been raised about why the flight was allowed to go ahead so soon after the typhoon.

"Many people were questioning why the plane took off in typhoon weather... according to my understanding the meteorology data showed that it met the aviation safety requirements," transport minister Yeh Kuang-shih told reporters.

Officials said that two planes had landed safely at Magong airport shortly before the disaster.

On Thursday, the scattered remains of the plane could be seen as more than 100 rescuers -- including firefighters and soldiers -- worked to remove bodies and debris from the scene.

- Relatives identify the dead -

It was not clear if all the bodies had been removed from the crash site.

At a nearby funeral home, dozens of relatives -- including the elderly and children -- sobbed as they waited to identify whether their loved ones had been killed.

Volunteers tried to comfort them as headshot photographs of the victims were posted on the wall to help with identification.

Penghu county deputy fire chief Hsu Wen-kuang said it took firefighters almost an hour to douse fires after the plane burst into flames on impact.

Investigators are looking into the cause of the crash, including why the plane was cleared to fly in bad weather.

The airline said the pilot was 60-year-old Lee Yi-liang who has 22 years of experience, accumulating nearly 23,000 flight hours.

The co-pilot was 39-year-old Chiang Kuan-hsin with two and a half years of experience.

As some relatives arrived in Penghu, others were seen waiting at the airports in Kaohsiung and Taipei to get on a flight to Penghu.

The mother of one survivor said: "My daughter called me. She said 'mum, my plane crashed'. She said she climbed out and borrowed a phone from others."

TransAsia, Taiwan's first private airline, also runs international flights to China, Japan, Singapore, South Korea and Vietnam. It is due to launch the island's first low-cost airline later this year.

TransAsia said it planned to compensate each family of the deceased with Tw$1 million ($33,000), and offer Tw$200,000 to each of the injured.

The last civilian plane crash in Taiwan was in 2002 when a China Airlines plane bound for Hong Kong crashed off Penghu islands into the Taiwan Strait, killing all 225 crew and passengers on board.

An ATR-72 operated by Lao Airlines crashed during a heavy storm in southern Laos in October 2013, killing all 49 people on board.