Spanish investigators on Thursday found two more bodies in the wreckage of a high-speed train involved in a devastating collision last weekend, later confirming the final death toll as 45.

The CID, the official body handling data following Sunday's crash, confirmed the final toll in a statement on Thursday evening.

An Andalusia emergency services spokesman had earlier said two bodies had been recovered from the train operated by state company Renfe, which smashed into another service by private firm Iryo that had derailed and crossed onto its track.

The collision, which also injured over 120 people, was followed by more rail accidents just days later.

The incidents have raised doubts about the safety of train travel in Spain, the European Union's fourth-largest economy and a top tourist destination boasting the world's second-largest high-speed network.

Spain observed three days of national mourning after Sunday's collision involving two high-speed trains in the southern region of Andalusia – the country's deadliest rail accident in more than a decade.

Rescuers found the last two bodies after conducting a "more thorough" search of two carriages "in a severely deteriorated condition", the head of the Civil Guard's investigative unit, Fernando Dominguez, told journalists.

Of the 45 people killed, all are Spanish apart from three women from Morocco, Russia and Germany, according to the CID.

Spain is searching for answers to what the transport minister has called an "extremely strange" disaster, which happened on a recently renovated stretch of straight, flat track and involved a modern Iryo train.

On Tuesday, a train driver died and 37 people were injured when a commuter service hit a retaining wall that fell onto the tracks near Barcelona in the northeastern region of Catalonia.

The second accident was thought to have been a consequence of recent heavy rainfall.

It prompted the suspension on Wednesday of all of the wealthy region's main Rodalies commuter network, used by hundreds of thousands of people, while safety checks were carried out.

Rodalies services were expected to resume on Thursday but remained suspended as only six of 140 drivers reported for work, said Catalan regional government spokeswoman Silvia Paneque.

Service will resume after inspections involving the drivers, she said, with no date set.

The secretary general of the Semaf train driver union, Diego Martin Fernandez, told RAC 1 radio that a thorough review of infrastructure had been agreed but that "the procedure had not been respected".

"To restore confidence that the infrastructure meets safety conditions, we need guarantees," he said, denouncing fresh landslips on the lines.

Semaf has called a national strike for February 9 to 11, denouncing repeated safety failings. Transport Minister Oscar Puente vowed to negotiate to have the strike called off and said the two tragedies were unrelated, defending the public transport system.

The list of incidents grew on Thursday after a commuter train in the southeastern region of Murcia hit a crane mounted on a truck, causing six light injuries. (AFP)