The exercise traveled north from Lisbon to Braga, with normal stops in the towns of Coimbra and Porto.
However, at around 15:30 (14:30 GMT), it crashed into a railway maintenance device in the city of Soure.
President Marcelo Rebelo de Sousa said he presented his “condolences to the family and friends of the deceased” in the “serious accident”.
The country’s national rescue firm, CNOS, told news firm Reuters that there were emergencies on the scene.
A spokesman said there were 163 rescuers, firefighters and two medical helicopters.
There are 240 passengers aboard the Alfa Pendular train, which is the fastest in Portugal, they said.
A witness told Portuguese newspaper Diio de Noticias that there had been panic in the exercise at the time of the accident.
“I think I’m going to die, ” they said. “It took 10 to 15 seconds for the car to stop. People were screaming and lying on the floor. Then the car started to fill with dust.
“We were trapped in the car, because the doors had been destroyed. Someone checked to break one and we went out and helped other people.”