The official death toll of Sunday's accident has risen to 40 with more than 150 believed to be injured.
Officials warn the count may not be definitive, with emergency workers still probing for bodies among what Andalusian regional president Juanma Moreno called "a twisted mass of metal".
Interior Minister Fernando Grande-Marlaska told Spanish national television RTVE that searchers believe they have found three more bodies still trapped in the wreckage.
Those bodies are not included in the official count, the minister said.
The crash took place Sunday at 7.45pm local time when the tail end of a train carrying 289 passengers on the route from Malaga to the capital, Madrid, went off the rails.
It slammed into an incoming train travelling from Madrid to Huelva, another southern Spanish city, according to rail operator Adif.
The head of the second train, which was carrying nearly 200 passengers, took the brunt of the impact.
That collision knocked its first two carriages off the track and sent them plummeting down a four-metre slope. Some bodies were found hundreds of metres from the crash site, Moreno said.
Officials are continuing to investigate the causes of the incident that Spanish Transport Minister Oscar Puente has called "strange", since it occurred on a straight line and neither train was speeding.
But Puente said late on Monday that officials had found a broken section of track.
"Now we have to determine if that is a cause or a consequence (of the derailment)," Puente told Spanish radio Cadena Ser.
The train that jumped the track belonged to the private company Iryo, while the second train, which took the brunt of the impact, belonged to Spain's public train company, Renfe.
Iryo said in a statement its train was manufactured in 2022 and passed its latest safety check on January 15.
Alvaro Fernandez, the president of Renfe, said both trains were travelling well under the speed limit of 250km/h and human error could be ruled out.
Spanish Prime Minister Pedro Sanchez visited the accident site near the town of Adamuz on Monday, where he declared three days of mourning with flags lowered on all public buildings and navy vessels.
Spain's King Felipe and Queen Letizia are scheduled to visit on Tuesday.
Meanwhile, Spain's Civil Guard is collecting DNA samples from family members who fear they have loved ones among the unidentified dead.
