Greek Prime Minister Kyriakos Mitsotakis on Wednesday said a "tragic human error" was likely responsible for a train collision that has left at least 38 dead in the country's worst rail tragedy.

Two carriages were crushed and a third engulfed in fire when a passenger train and a freight train late Tuesday collided near the central city of Larissa, on a route plagued by years of safety warnings.

The fire department had earlier increased the death toll to 38, adding that 57 people were still hospitalised, six of them in intensive care, while several were missing.

"Everything shows that the drama was, sadly, mainly due to a tragic human error," Mitsotakis -- who is seeking re-election this year -- said in a televised address.

He said it was a "terrible train accident without precedent" in Greece which would be "fully" investigated.

"I've never seen anything like this in my entire life," said one rescue worker, emerging from the wreckage. "It's tragic. Five hours later, we are finding bodies." 

The accident left a tangled mess of metal and shattered glass in a field.

In some cases, passengers are being identified from body parts, volunteer fireman Vassilis Iliopoulos told Skai TV, warning that the death toll would rise.

Seventeen biological samples have been collected from remains, and from 23 relatives seeking a match, the police said.

"It was the train of terror," Pavlos Aslanidis, whose son is missing along with a friend, told reporters.

Greece's transport minister submitted his resignation just hours after the accident.

"When something so tragic happens, we cannot continue as if nothing had happened," Kostas Karamanlis said in a public statement.

On Wednesday evening, police in the capital Athens fired tear gas at protesters throwing rocks at the offices of the railway's operating company, Hellenic Train.

- Years of safety concerns -

The passenger train, carrying more than 350 people, had been travelling from Athens to the northern city of Thessaloniki.

The 59-year-old station master of Larissa was arrested several hours after the accident and charged with negligent homicide.

Government spokesman Yiannis Economou said the two trains were left running on the same track for "several kilometres".

But train unionists said the station master was likely a scapegoat as the safety shortcomings of the Athens-Thessaloniki railway line had been known for years.

In an open letter in February, train staff said track safety systems were incomplete and poorly maintained. 

A safety supervisor had resigned last year, warning that infrastructure upgrades pending since 2016 were incomplete and that train speeds of up to 200 kilometres (124 miles) an hour were unsafe.

The president of the train drivers' union Kostas Genidounias told AFP from the scene that the accident "would have been avoided if the safety systems were working".

- 'Complete panic' -

Health Minister Thanos Plevris said most passengers were "young people", with the train carrying many students returning to Thessaloniki after a long holiday weekend. 

"It was a nightmare... I'm still shaking," 22-year-old passenger Angelos told AFP.

"Fortunately we were in the penultimate car and we got out alive. There was a fire in the first cars and complete panic.

"The collision was like a huge earthquake."

"I was stained with blood from other people who were injured near me," a passenger named Lazos told the newspaper Proto Thema.

Some 150 firefighters and 40 ambulances were mobilised for the response, according to Greek emergency services.

Crews were still struggling to lift one of the smashed carriages, lying on its side, to enable a search inside, Iliopoulos said.

"My thoughts are with the people in Greece this morning," tweeted the head of the European Council, Charles Michel. 

"Shocked by the news and images of the collision of the two trains," he added.

Neighbouring Albania, Italy, Serbia and Turkey were among states to send condolences, as did China, the United States, France, Russia, Ukraine, Germany, and the Vatican.

Nicosia said two Cypriots were among the missing.

- 'Windows exploded' -

On the local media site Onlarissa, a young woman said that the train "was stopped for a few minutes when we heard a deafening noise".

Another passenger told Skai TV that "the windows suddenly exploded. People were screaming."

"Fortunately, we were able to open the doors and escape fairly quickly. In other wagons, they did not manage to get out, and one wagon even caught fire," he added.

Authorities have declared three days of national mourning.