Rescuers continued digging through debris on Saturday at the site of Greece's worst train crash but were expected to wrap up their search operation later on the day.

Tuesday's crash killed at least 57 people and injured dozens when a passenger train with more than 350 people on board careered into a freight train on the same track.

The disaster in central Greece has triggered an outpouring of anger and protests across the country, as well as a sharp focus on safety standards across its railway system.

The station master of the nearby city of Larissa has been arrested over the disaster, which the government has blamed on human error but which railway workers' unions say was inevitable because of deficient safety systems and understaffing.

He was expected to appear before a prosecutor on Saturday to respond to felony charges of disrupting transport and putting lives at risk.

The train, traveling from Athens to the northern city of Thessaloniki, was packed with students returning after a long holiday weekend.

Police said 54 bodies out of 56 people reported missing by relatives had so far been identified - almost all from DNA tests as the crash was so violent. A 57th body has not been identified as no one has appeared so far to give a DNA sample.

Bereaved families have vowed to seek justice.

"It is a very difficult situation," a relative told Greece's Skai radio. "We will see how we will move (legally), we won’t let anything go, the families’ demand is that they don’t get away with it."

Railway workers union have staged 24-hour walkouts since Wednesday. They extended labour action by 48 hours on Friday, demanding a clear timetable by the government for the implementation of safety protocols.

On Friday, police and protesters clashed after 2,000 students marched through Athens, blocking the road in front of parliament for a moment of silence. Students also demonstrated in Larissa and Thessaloniki.