Thousands of Greeks have taken to the streets for a second day of protests as anger mounts over the loss of life in Tuesday night’s head-on train crash.

Braving torrential rain and thunder, demonstrators marched from the office headquarters of Hellenic Train in Athens to the Greek parliament, chanting “this crime will not be forgotten”.

Many were as young as the vast majority of those killed in the collision between a passenger train and a freight train. Of the 57 confirmed dead so far, almost all were students. Late on Thursday, authorities announced that another 56 people on the passenger list were still missing.

“They’ll try to cover it up but we’re not going to let them,” said Stelios Dormarazoglou, pulling his hood tight around his head and shouting “the dead will become one voice, their blood will pursue you”!

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He said: “Everyone knows that if the Greek state had wanted, this accident could have been prevented. My own son worked on upgrading the signalling system — nine years ago. Ever since it’s been stalled because companies are only ever interested in profits.”

The protests came hours after the centre-right government of prime minister Kyriakos Mitsotakis conceded that rail projects nationwide had been beset by “chronic public sector ills”.

In the first public admission of the problems plaguing the railway network, officials said efforts to overhaul the system had failed. “We are all devastated by this tragic incident,” Giannis Oikonomou, a government spokesperson, told a news conference. “The loss and trauma this caused, the physical and mental trauma of survivors, and the angst of this country is huge, and it’s difficult to manage, particularly now.”

As rescue teams resumed the painstaking process of looking for the dead in the worst-damaged wagons, Mr Oikonomou said authorities would look into the causes of the accident and delays in implementing rail projects, which he said were “rooted in chronic ills of the Greek public [sector] … which the government has not managed to eradicate”.

Highlighting the growing sense of fury over the crash, outside Tempe in central Greece, protesters hurled rocks at the Athens rail company offices on Wednesday evening before being dispersed by volleys of teargas fired by riot police. Protests also broke out in Thessaloniki.

On Thursday, railway and metro workers went on strike. In a statement, unions said the stoppage — which is to be extended until Saturday — had been called to protest against the “disrespect that [successive] governments have shown towards the Greek railroads which led to the tragic result in Tempe”. Unions say cost-cutting, staff shortages, antiquated equipment and impoverished infrastructure have plagued the network for years.

Hellenic Train was among the many public utilities privatised at the height of Greece’s long-running debt crisis.

A Greek magistrate called for an urgent inquiry into allegations that a long stretch of track leading to Athens international airport, used by millions of foreign tourists every year, is operated with inadequate signalling. The charges were made by the Federation of Railroad employees, with leading figures going on television to call for action.

The rescue operation has been made especially difficult because workers have had to rely on special cutting machines to disentangle the mangled wreckage. At the time of the crash, at 11.20pm on Tuesday, several students are believed to have been gathered in the restaurant car, in the second carriage, which took the full force of the collision.

They had boarded the Thessaloniki-bound night train in the Greek capital after a three-day holiday weekend. “It was a student train, full of kids … in their 20s,” Costas Bargiotas, a senior orthopaedic doctor at Larissa general hospital, told Skai TV. “It was truly shocking … the carriages crumpled like paper.”

Although the search is expected to continue in the days ahead, any prospect of finding survivors has all but evaporated, said emergency workers. Temperatures would have exceeded 1,300 degrees in the front two carriages when they exploded into flames.

Witnesses who rushed to the site of the accident, 235 miles north of Athens, discovered a scene of devastation. Passengers who managed to flee the train, or were ejected through carriage windows, spoke of chaos and panic. One survivor described the terror of having to make a split-second decision of “either being burned alive or jumping and breaking all my bones”. She was among 66 injured people taken to hospital. At least six of the wounded are on life support.

The grim process of identifying the victims has been made more complicated, according to media reports, because forensic scientists, for the most part, have only had incinerated body parts with which to work. Relatives desperately seeking loved ones have had to provide DNA samples so that corpses can be matched and handed over to families. The health ministry said relatives had been prevented from seeing the bodies “for psychological reasons”.

Greece has been plunged into nationwide grief, with Mr Mitsotakis ordering that flags fly at half-mast for an official three-day mourning period.

“We are living through especially dark days for our country,” said newly assigned transport minister Giorgos Gerapetritis, addressing reporters as he replaced Kostas Karamanlis, who resigned from the post “in memory of the victims” on Wednesday. “After this tragic accident, the country is going through extremely hard times.”

Mr Mitsotakis has promised an independent investigation by an all-party committee of experts.

In the almost 48 hours since the crash, much of the blame has been attributed to the stationmaster at Larissa, the nearest city to the crash site. On Thursday, his lawyer said while the 59-year-old rail employee was willing to assume some responsibility for the disaster, other factors were also at play.

Stefanos Pantzartzidis said his client, who was arrested in the aftermath of the crash, had been charged with disrupting transport and putting lives at risk.

“He is literally devastated,” said Mr Pantzartzidis. “Since the first moment, he has assumed responsibility proportionate to him … [but] there has been convergent negligence by many other factors.”

Although Mr Mitsotakis and others in his administration have been quick to blame “human error”, there is a growing and widespread belief that the crash could have been prevented.

“It is not a mistake, it’s a crime,” declared the opposition Syntakton newspaper in a banner front-page headline, noting that railway unions had long warned of the system’s inherent dangers.

A recording of the communication between the train driver and the stationmaster which was published on Proto Thema website suggested the latter told the driver to continue past a red signal.

“Is Larissa listening?” the driver said referring to the stationmaster, according to the recording.

“It is listening ... pass the red signal at the exit until the entrance signal at Neoi Poroi [station],” the stationmaster responded.

But that order did not strike the driver as strange as the signalling system had been dysfunctional, Proto Thema reported. — Guardian/Additional reporting: Reuters