The Greek transport minister has resigned and a station master has been charged with manslaughter as it emerged “tragic human error” was to blame for a deadly head-on collision between two trains.

Rescue workers continued to search for survivors on Thursday after the fiery crash that killed dozens of people and left scores injured, raising questions about Greece’s poor track record of railway safety.

The passenger train carrying 350 people and cargo train were travelling on the same tracks in central Greece when they crashed, throwing entire carriages off the line.

Officials said the death toll of 38 it could rise further as temperatures in one carriage reached 1300 degrees when it was engulfed in flames.

Passengers described a “nightmarish” crash like an earthquake that shattered their train and created an inferno just before midnight near the central town of Larissa.

It was headed to the northern city of Thessaloniki, from the capital Athens, after a long holiday weekend.

Some passengers were thrown up to 40 metres on impact while others who were trapped kicked through windows to escape the flames.

The local station master, in charge of signalling, was arrested and charged with causing mass deaths through negligence and causing grievous bodily harm through negligence, a police official said.

The 59-year-old man has denied any responsibility for the accident, attributing it to a possible technical failure, an official said.

The two trains had been running towards each other on the same track “for many kilometres” before the crash, government spokesman Giannis Oikonomou said.

Yiannis Ditsas, head of the Greek railway workers union, told Skai television that automatic signalling at the spot of the crash had not been working.

There was no immediate official comment on this.

Police and emergency crews search the wreckage. Photo: Getty

Greek Prime Minister Kyriakos Mitsotakis said it was an “unthinkable tragedy” and blamed human error.

“Our thoughts today are with the relatives of the victims,” Mr Mitsotakis said at the site of the crash, looking shattered.

“Everything shows that the drama was, sadly, mainly due to a tragic human error,” he later said in a televised address.

Greek Transport Minister Kostas Karamanlis submitted his resignation, saying he was taking responsibility for the state’s “long-standing failures” to fix a railway system he said was not fit for the 21st century.

“It is a fact that we received the Greek railway system in a state that is not up to 21st century standards,” Mr Karamanlis said, adding that in the past three-and-a-half years the government had “made every effort to improve this reality.”

“Unfortunately, our efforts have not been sufficient to prevent such a bad incident. And this is very heavy for all of us and me personally.

“I hand in my resignation as transport and infrastructure minister. It is what I feel is my responsibility to do as the minimum sign of respect to the memory of the people who died so unjustly.”

Fire brigade spokesman Vassilis Varthakogiannis said the temperatures in the first carriage made it hard to identify those trapped inside or say how many died exactly.

“There was panic… the fire was immediate, as we were turning over we were being burned, fire was right and left,” Stergios Minenis, a 28-year-old passenger who jumped to safety from the wreckage, said.

Another passenger, who escaped from the fifth carriage, told Skai TV: “Windows were being smashed and people were screaming… One of the windows caved in from the impact of iron from the other train.”

Flags flew at half-mast in Athens, as well as in Brussels, in a tribute to the victims of the crash, as the government declared three days of mourning.

In Larissa, where many victims of the crash had been taken, Nikos Makris sat on a pavement outside the hospital.

His wife’s sister was travelling in one of the first two carriages.

“She is missing. We have been waiting here since 2am,” he told Reuters.

“Now we are waiting to do a DNA test. We will be lucky to have a body to bury,” he said.

Others were angry. The relative of one victim shouted: “Some bastard has to pay for this.”

The head of the emergency unit in Larissa hospital, Apostolos Komnos, said most of the dead were young people, in their 20s.

The passenger train was carrying 342 travellers and 10 crew while two crew were on the cargo train, according to Hellenic Train data.

Sixty-six of those injured were hospitalised, six of whom in intensive care, a fire brigade official said.

The cargo train had been travelling from Thessaloniki to Larissa.

Local media said the train left Athens about 7.30pm.