The death toll in Spain's deadliest rail disaster in over a decade rose to 41 Tuesday, as the country began three days of national mourning for the victims of the high-speed collision.

The crash took place near Adamuz in the southern Andalusia region late Sunday night, when a high-speed train operated by private rail company Iryo, going to Madrid from Malaga, derailed, straying into the path of an oncoming train operated by Spain's public Renfe network, which also then derailed.

The cause of the crash remains a mystery, though investigators say they will focus on coach six of the Iryo train, which they believe was the first to derail. The Guardia Civil national police force asked for that carriage to be left where it came to a rest so it can be examined.

Rail experts "extremely surprised" by crash on straight track

"There are many pieces of the puzzle we must fit together," Spain's Transport Minister Oscar Puente told the country's Onda Cero radio network Tuesday.

Puente called the crash "extremely strange" on Monday because it happened on a flat stretch of track that had been renovated in May, adding that "all the railway experts are extremely surprised."

"Nothing seems to suggest anything was wrong with it," he said Tuesday, adding that freshly laid track can sometimes exhibit "youthful sins."

Investigators studying the scene of the accident found a broken joint on the rails, which likely created a gap that widened as trains passed over it, the Reuters news agency said Tuesday, citing a source briefed on the initial investigation. The faulty joint could prove key to determining the cause of the accident, the source said.

Puente, however, warned against drawing any conclusions based on "mere speculation."

"When the train went off the rails, it produced a ton of fractures in the track, for about 200 meters [yards]. And so for the first fracture in the track, the key is to determine — and currently no expert can say for certain — if this fracture was a cause or a consequence," he told Onda Cero.

"That is the crux of this whole thing, or one of them, knowing what came first — the fracturing of the track and then the derailment, or if the derailment caused the fracture in the track," Puente said, adding that if there was an issue with the track before the crash, investigators would still "have to find out why."

Spain's chief high-speed train engineer Álvaro Aznar told CBS News on Monday that the "earliest signs point to mechanical failure" as the cause of the crash, but authorities have stressed that it could take weeks, if not longer, to know for sure.

Death toll could still climb as recovery work continues

Residents were among the first on the scene. 

"There were people with missing limbs," said one man, who shuttled survivors to safety on his four-wheeler. "They were crying. Nobody was born to see this." 

The death toll from the accident climbed to 41 on Monday evening after the body of another passenger was found in one of the Iryo train carriages, according to the the regional government.

More than 120 people were injured and 39, including four children, were still hospitalized on Tuesday as the nation began three days of mourning. 

Across the country, public buildings flew flags at half-mast, while television anchors wore black, and cabinet ministers cut back public appearances.

Rescue crews began using heavy machinery to lift some of the worst damaged train coaches off the damaged section of track on Monday, to give better access to the site.

Juan Manuel Moreno, the head of the Andalusia region's government, said Monday that it would take another 24-48 hours "to know with certainty how many deaths have resulted from this terrible accident."

Spain's King Felipe VI and Queen Letizia visited the town of Adamuz on Tuesday to meet with rescue workers and officials.