The latest reports from the National Fire Agency say 490 people were on the train, with 41 dead and more than 60 injured.
"This is our initial understanding and we are clarifying the cause of the incident", he added.
The train, from the capital Taipei to Taitung, was carrying people travelling for a long-weekend annual holiday.
Survivors described their terror as the train slammed into the truck and ground to a halt.
The accident occurred on Taiwan's eastern railway line around 9:30am (0130 GMT).
Other pictures online showed people walking along the tracks with their belongings as they were evacuated from less badly affected carriages.
The Central Emergency Operation Center gave a lower suspected death toll of 26 people showing no signs of life.
"Many people were crushed under train seats in the collision".
Images showed an injured passenger carried away on a stretcher, with her head and neck in a brace, while others gathered suitcases and bags in a tilted, derailed carriage as some walked on the train's roof to exit the tunnel.
She later told reporters that she will do all she can to provide the maximum support for the survivors and families of the deceased.
Media reported 350 passengers were on board.
The accident occurred at the beginning of a long weekend for the traditional Tomb Sweeping Day holiday.
During the festival, people return to ancestral villages to tidy up the graves of their relatives and make offerings.
Taiwan's eastern railway line is usually a popular tourist draw down its dramatic and less populated eastern coastline.
With the help of multiple tunnels and bridges, it winds its way through towering mountains and dramatic gorges before entering the picturesque Huadong Valley. He said the crash was the worst-ever in Taiwan.
The driver of the eight-carriage train was later charged with negligent homicide.
A train partially derailed along Taiwan's east coast on Friday, with dozens of people feared dead.
In 1991, two trains collided in Miaoli County, western Taiwan, resulting in 30 fatalities and injuring more than 100.
Taiwanese railway officials will be required to conduct sweeps along other tracks in the system to "prevent this from happening again", Su Tseng-chang, the country's premier, said.