The passenger train and a freight train slammed into each other late on Tuesday, crumpling carriages into twisted steel knots and forcing people to smash windows to escape.

It was the country’s deadliest crash ever, and 48 people remained hospitalised, most in the central Greek city of Larissa.

Six of them were in intensive care.

Fire Service spokesman Yiannis Artopios said the grim recovery effort was proceeding “centimetre by centimetre”.

“We can see that there are more (bodies) people there. Unfortunately they are in a very bad condition because of the collision,” Artopios told state television.

The cause of the crash is still not clear.

The Larissa station manager arrested after the collision was charged on Wednesday with multiple counts of manslaughter and causing serious physical harm through negligence as a judicial inquiry tries to establish why the two trains were travelling in opposite directions on the same track.

Railway workers’ associations, meanwhile, called strikes, halting rail services across the country and the subway in Athens.

They are protesting working conditions and what they described as a dangerous failure to modernise the Greek rail system due to a lack of public investment during the deep financial crisis that spanned most of the previous decade and brought Greece to the brink of bankruptcy.

“Unfortunately, our long-standing demands for full-time staff hirings, better training and above all, implementation of up-to-date security systems have always ended up in the wastepaper basket,” Greece’s federation of railway employees said in a statement announcing Thursday’s strike.

Transport Minister Kostas Karamanlis resigned following the crash, his replacement tasked with setting up an independent inquiry looking into the causes of the crash.

“Responsibility will be assigned,” Prime Minister Kyriakos Mitsotakis said in a televised address after visiting the collision site.

“We will work so that the words ‘never again’… will not remain an empty pledge,” he said.

“That I promise you.”

More than 300 people were on board the passenger train, many of them students returning from a holiday weekend and annual Carnival celebrations around Greece.

Andreas Alikaniotis, a 20-year-old survivor of the crash, described how he and fellow students escaped from a jack-knifed train car as fire approached, smashing windows and throwing luggage onto the ground outside to use as a makeshift landing pad.

“It was a steep drop, into a ditch,” Alikaniotis, who suffered a knee injury, told reporters from his hospital bed in Larissa.

“The lights went out… The smoke was suffocating inside the rail car but also outside,” Alikaniotis said.

He said he was “one of the few around who had not been seriously injured”.

“Me and my friends helped people get out.”

Relatives of the victims and still-missing passengers lashed out at government officials and Italian-owned private rail operator Hellenic Train.

Dimitris Bournazis, whose father and 15-year-old brother remain unaccounted for, said phone calls to the rail company have been fruitless.

“I’ve been trying since yesterday afternoon to communicate with the company to find out what seat my father was in,” he said.

“Nobody has called me back.”

He has lost hope of seeing either of his loved ones alive again.

“I’ve lost my brother, my father. That can’t change, I know it,” he said.

“But the point is for us not to mourn victims like that again. They bought 50 tickets to death.”

Bournazis said responsibility for the crash should go far beyond the station master.

“We can’t dump all the blame on one person for making one mistake,” he said.

-with AAP