Protests were also held in Thessaloniki and the city of Larissa, near where the disaster happened on Tuesday night.
The government has said an independent investigation will deliver justice.
Three days of national mourning have been declared across the country following the incident, in which a passenger service crashed head on into a freight train, causing the front carriages to burst into flames.
The front carriages of the passenger train were mostly destroyed.
Many of the 350 passengers on board were students in their 20s returning to Thessaloniki after a long weekend celebrating Greek Orthodox Lent.
Prime Minister Kyriakos Mitsotakis said "tragic human error" was to blame for the disaster.
A 59-year-old station master in Larissa has been charged with manslaughter by negligence. He has denied any wrongdoing, blaming the crash on a technical fault.
Rail union members believe
safety systems were not working properly, with repeated warnings about this over many years.
In protest and mourning, rail workers are planning on striking on Thursday at what they say is official neglect of the railways.
"Pain has turned into anger for the dozens of dead and wounded colleagues and fellow citizens," the workers' union said in a statement announcing the strike.
"
The disrespect shown over the years by governments to the Greek railways led to the tragic result," it added in comments cited by Reuters news agency.
Transport Minister Kostas Karamanlis resigned over the disaster, saying he would take responsibility for the authorities' "long-standing failures" to fix a railway system he said was not fit for the 21st Century.
But outside a hospital where bodies of the train crash's victims were being brought, a banner was hung claiming that any systemic failings would be covered up in the official investigation now under way.
At a silent vigil in Larissa on Wednesday to commemorate the victims of the incident, one demonstrator said he felt the disaster had only been a matter of time.
"The rail network looked problematic, with worn down, badly paid staff," Nikos Savva, a medical student from Cyprus, told AFP news agency.
The station master arrested should not pay the price "for a whole ailing system", he added.
"
This is an inadmissible accident. We've known this situation for 30 years," a doctor based in Larissa, Costas Bargiotas, told AFP.
A vigil was also held in Athens, outside the offices of Hellenic Train. Later in the day, things turned violent in the same area, with police using tear gas to disperse protesters who threw stones and lit fires in the streets.
At the site of the country's worst ever train crash, rescuers yet again worked through the night.
Families have been arriving at a nearby hospital to give DNA samples so that their missing loved ones may be identified.
But this will become an increasingly difficult process as more remains are retrieved of those who were at the front of the passenger train and who bore the full force of the head-on collision and the fire that then ripped through their carriages.
Fire brigade spokesperson Vassilis Varthakogiannis said
temperatures inside the first carriage had reached 1,300C (2,370F), which made it "hard to identify the people who were inside".
IMAGE SOURCE,AFP
Image caption,
People lit candles and laid flowers outside the railway station in Larissa on Wednesday
IMAGE SOURCE,GETTY IMAGES
Image caption,
Protesters gathered outside the offices of Hellenic Train in Athens
IMAGE SOURCE,GETTY IMAGES
Image caption,
Candles were lit outside the offices in Athens
IMAGE SOURCE,AFP
Image caption,
Protesters clashed with police outside the Hellenic Train headquarters in Athens
www.sott.net
