The toll death from a Taiwan TransAsia Airways plane that crashed into the Keelung River in Taipei has risen to 31, of them six from the mainland.

The bodies of the pilot, co-pilot and a crew member were found in the water and two other passengers were discovered half a kilometre away in the river.

Rescuers continued to search for the 12 missing people from the plane that clipped a bridge, ten minutes after takeoff.

A total of 15 survivors have been taken to nearby hospitals in Taipei and New Taipei City, according to local disaster relief authorities. The plane's two black boxes have been recovered and should be deciphered by Wednesday night.

Using a massive crane, rescuers had last night pulled the three pieces of Flight GE235 from the Keelung River, Taiwan's central news agency reported. The fuselage and tail were brought to shore a little after 8 pm, and the nose was lifted just after midnight, according to Taipei City Fire Department officials.

Flight GE235 was headed for Kinmen from Taipei with 53 passengers on board, including 31 from the Chinese mainland, and five crew. Three of the mainland passengers are known to be children. According to latest information from Taiwan authorities, six of the 31 mainland passengers are confirmed dead and three others injured.

The plane has been in service since April 2014 and was subject to a routine safety check last month, according to Taipei authorities.

The aircraft plunged into the river at 10:55 am after its wing clipped a taxi with a man and a woman inside on an elevated freeway.

The mainland passengers were on trips organized by two travel agencies from Xiamen City in Fujian Province, the Taiwan tourism authority confirmed.

Xiamen police have fastracked travel documents for families of the mainland tourists on board so they can leave for Taiwan as early as possible. Thirty-four relatives of the victims, along with officials of Xiamen Tourism Bureau, are expected to arrive in Taiwan tomorrow.

Xiamen has set up an emergency team and seven city officials will travel to Taiwan as soon as possible to support the families.

Huang Wensheng, a Xiamen resident whose wife and son were on board was waiting for the travel permit at the Exit-Entry Administration of Xiamen Public Security Bureau on Wednesday afternoon. "I have not been able to get in touch with them," he said.

The Taiwan Work Office of the Communist Party of China (CPC) Central Committee has sent a team to Taiwan to handle related affairs.

The State Council Taiwan Affairs Office and the Association for Relations across the Taiwan Straits (ARATS) launched a joint emergency response operation and are being kept up to date by Taiwan's Mainland Affairs Council and the Straits Exchange Foundation (SEF). They extended condolences to families of the victims and urged those on the ground to do as much as they could.

In a message to the SEF, ARATS said families of the Chinese mainland passengers on board the plane are anxious to know their relatives' whereabouts and hoped that the SEF would assist in providing information.

After the crash, a total of 1,551 people, 394 vehicles and 77 boats had been sent to the riverside rescue scene by 7:00 pm on Wednesday.

Taiwan's civil aeronautics authority has decided to conduct safety check on the island's 22 ATR-72 aircraft before they are allowed to fly.

It was not the first time that the ATR-72 aircraft had crashed in Taiwan. On July 23, 2014, TransAsia Airways flight GE222, also an ATR-72 aircraft, crashed on Taiwan's Penghu islands, killing 48 people.

TransAsia Airways, founded in 1951, was Taiwan's first private airline, mainly focusing on short overseas flights.