The train was carrying 366 passengers when the accident occurred just before 5 pm local time, the transport ministry said.
The Chinese-language United Daily News (UDN) reported that rescue workers found many body parts near the sixth train vehicle.
Taiwan's central government said that the premier had been notified about the situation, Reuters report.
Some passengers were crushed to death, Ministry of National Defence spokesman Chen Chung-chi said.
While the malfunction itself is unlikely to trigger an acceleration, the TRA is also considering the possibility that the automatic train protection (ATP) system was turned off manually, said director-general Lu Chieh-shen (鹿潔身). "They were crushed, so they died right away", he said.
Images from the site showed the Puyuma Express train lying zigzag across the track.
Most of the deaths were in the first auto, which flipped over, a government spokesman said.
Hundreds of rescuers and military personnel worked through the night, using spotlights to search the wreckage for survivors, as ambulances waited to take the injured to hospital.
Whether the derailment was caused by human error or technical malfunction remains under probe, Central News Agency reported citing Wu Tze-cheng, head of the task force set up to investigate the fatal accident.
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An investigation was underway to find out the cause of the accident, Taiwan Railways Administration said.
Passengers who survived the accident recalled how the train had been shaking intensely during the journey and was going "very fast" before it derailed, reported Agence France-Presse.
Panic and shock after a train derailed in northeastern Taiwan on Sunday in the island's worst rail disaster in more than three decades.
At the scene, searchers walked through an upright auto with flashlights. "We will make the whole thing transparent'".
"We felt that the speed was too fast, then there was a crashing sound and we flew off [from the seats]", she said, adding many passengers were sleeping at the time.
Four carriages overturned in the crash.
The rail authorities said the train could hit a maximum speed of 130kmph.
Of the total injured, seven were still receiving intensive hospital care this morning. Five people were killed.
The train was operated by the Taiwan government-run train system and its cars, purchased from Nippon Sharyo Ltd., a leading Japanese manufacturer of railway carriages, entered service in 2013. Investigators blamed brake failure.