The Civil Guard said it had received reports of 64 people missing in what is already Spain's deadliest train accident since 2013.
Authorities have carried out 49 autopsies and identified five people, three women and two men, Esther Padilla, spokesperson for the Castilla-La Mancha regional government, said on state television network TVE.
"Testing is proceeding slowly, although families will be contacted throughout the day so that they can come and collect their results," Padilla said on Friday.
It's unclear how many of the missing were among the bodies still to be identified.
The crash, which happened near the town of Urda in central Spain, followed another fatal accident in January involving the same rail companies on the same line.
It has reopened a debate about safety and maintenance on Spain's high-speed rail network, the most extensive in Europe.
The collision occurred after several trains were automatically stopped due to the failure of the automatic signalling system, after which the central control centre in Madrid took over.
A train operated by state-owned Renfe was authorised to proceed, even though there was a stationary Iryo-operated train ahead, according to Transport Minister Oscar Puente.
Audio of communications between the control centre and the train drivers obtained by El Pais showed how a controller authorised the Renfe train to continue on its journey at a normal speed, which Puente said disregarded a protocol to travel at no more than 40km/h in such circumstances.
The audio also showed the controller authorised the Renfe train, carrying 379 passengers and seven crew, to renew its journey when it should have been the Iryo train in front, which carried 147 passengers and five crew, to proceed first, according to protocol.
"The sequence of malfunctions, instructions, and actions eventually led to the collision, in the absence of the necessary mitigating barriers," according to the preliminary report by the Independent Authority for the Technical Investigation of Accidents and Incidents (AITAT).
It estimated the Renfe train was travelling between 160km/h and 200km/h when the collision occurred.
AITAT said it would not be able to confirm the exact speed of the train until it extracted information from the train's black box.
"The scene was devastating. You saw carriages completely burnt out, as if they'd exploded. What you see coming out were people in a very bad way, and others who start pulling out the bodies of the deceased and placing them right there next to where we were," Sebastian Herrero, who was travelling near the front of the Iryo train, said.
