There are suggestions that the train driver may have been ill or unconscious at the controls, according to regional Infrastructure Minister Jose Ramon Garcia Anton.
He told reporters in Valencia that at the moment of the accident, the black box recorder showed the train was travelling "too fast", at 80 kilometres an hour on a curve on which there is a speed limit of 40 kilometres an hour.
"All other possibilities (to explain the accident) are ruled out, " he said after a meeting between the unions, metro safety staff and the head of the Valencia metro, the responsibility of the regional government.
"The tunnel did not cave in", nor "was it damaged", the wheels were "in perfect condition" and the "carriages were not too full," he said.
The black box also showed that the train driver, who died in the accident, "did not react to the speed" and "there must have been a sort of loss of consciousness, of fainting," railway trade union spokesman Jose Aroca said after the meeting.
A five-minute silence was observed across Spain in memory of those who died in the accident -- 29 women and 12 men.
All but one of them have been identified.
One of the 39 injured people is an 11-year-old girl whose mother died in the crash, according to Valencia official Luis Felipe Martinez.
Another is a pregnant woman whose condition was described as critical.
There were five foreigners among the dead: an Argentine man, a Bulgarian woman, a Colombian woman, a Paraguayan man and a Venezuelan man.
King Juan Carlos, Queen Sofia and Prime Minister Jose Luis Rodriquez Zapatero -- who cut short a visit to India -- attended a mass for the victims at Valencia Cathedral late on Tuesday, followed by hundreds of people outside on a giant screen.
"The pope sends his condolences and thinks of you and prays for you," Archbishop of Valencia, Agustin Garcia-Gasco, told mourners.
More than a million pilgrims are gathering in Valencia, four days before Pope Benedict XVI is due to visit for the Roman Catholic Church's fifth World Family Meeting.
Two cranes above ground at a location corresponding to the crash site below were set up to use cables lowered through a hole cut in the blacktop to straighten up and then tow the derailed train cars.
The cranes were installed between rows of eight-storey brick buildings draped with the Vatican's white-and-yellow flags.
With Spain still shaken by the Madrid train bombing of 2004 that killed 191 people, officials were quick to exclude foul play in Valencia.
An interior ministry spokesman said any terrorist link has been "completely ruled out".
A meeting scheduled Tuesday between the Basque branch of Spain's ruling Socialist Party and the banned political wing of the armed regional separatist movement ETA was cancelled following the Valencia disaster, Spanish media reported.
The train had passed a safety inspection just one week before the crash, according to reports from Spain's Efe news agency.
Unions said the train line where the accident happened is the oldest in Valencia's metro network.
Last September, three underground trains collided in Valencia on the same line, injuring 29 people.