Many of the victims were thought to be university students returning home late on Tuesday after a long holiday weekend. Officials said the death toll was expected to rise further - temperatures in one carriage had risen to 1300C after it caught fire.
Authorities are working to establish how the high-speed passenger train collided with another carrying shipping containers, coming in the opposite direction and on the same track at speeds thought to be up to 160 kilometres per hour.
"Everything in this tragedy points, unfortunately, mainly to human error," Greek Prime Minister Kyriakos Mitsotakis said in a televised address on Wednesday.
Passengers described a "nightmarish" crash which engulfed their train in flames just before midnight near the central town of Larissa, some 320km north of Athens. It had departed from the Greek capital and was headed to the northern city of Thessaloniki.
Some kicked through windows to escape the inferno. Others were flung up to 40 metres on impact.
A station master was arrested as investigators tried to determine why the two trains had been on the same track "for many kilometres", while the country's transport minister resigned.
As rescuers scoured the smouldering, mangled mass of steel in the morning, cranes lifted window-less carriages.
Fire brigade spokesman Vassilis Varthakogiannis said the temperatures in the first carriage made it difficult to identify those trapped inside, or say how many died. Based on that, the death toll was likely to rise, he said.
Flags flew at half-staff in Athens and in Brussels and the Greek government declared three days of national mourning.
"It's an unthinkable tragedy. Our thoughts today are with the relatives of the victims," Mitsotakis, looking shattered, said at the site of the crash.
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."
In later statements he said he had accepted the resignations of senior officials in rail operator OSE and its subsidiary ERGOSE. In Athens, about 1000 people protested outside the offices of Hellenic Train, another branch of the rail network, where some hurled stones at windows.
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.
The local station master, in charge of signalling, has been charged with causing mass deaths through negligence and causing grievous bodily harm through negligence, a police official said.
The 59-year-old man denied any responsibility, attributing the accident to a possible technical failure, the official said.
Yiannis Ditsas, head of the railway workers union, told Skai TV that automatic signalling at the site of the crash had not been working. There was no immediate official comment.
The passenger train was carrying 342 travellers and 10 crew, with two crew on the cargo train, Hellenic Train data showed.
There were 66 people taken to hospital, six of whom were in intensive care.
Another woman said her child was not picking up the phone.
Greece sold railway operator TRAINOSE to Italy's Ferrovie dello Stato Italiane in 2017 as part of its international bailout program, expecting hundreds of millions of euros to be invested in rail infrastructure in the coming years.
The Italian division maintained responsibility for passenger and freight, while the Greek state controlled infrastructure.
