A small group of protesters hurled petrol bombs at police, who responded with tear gas and hand grenades, before dispersing to nearby streets.
At least 57 people were killed and dozens were injured on Tuesday when a passenger train with more than 350 people on board collided with a freight train on the same track in central Greece.
After protests over the past three days across the country, some 10,000 students, railway workers and groups affiliated with leftist parties gathered in an Athens square on Sunday to express sympathy for the lives lost and to demand better safety standards on the rail network.
Protesters shouted, "That crime will not be forgotten," as they hurled black balloons into space. Placard: "Their policies have cost lives."
The train, travelling from Athens to the northern city of Thessaloniki, was packed with university students returning after a long holiday weekend. The disaster has triggered an outpouring of anger, as well as a sharp focus on safety standards.
Railway workers who lost their colleagues in the accident have been staging rotating walkouts ever since Wednesday to protest cost-cutting, underinvestment in rail infrastructure and a legacy from Greece's crippling debt crisis between 2010 and 2018.
The crash was attributed to human error by Prime Minister Kyriakos Mitchellsakis' government. Mitsotakis stated on Sunday that the blame for the crash should not be shifted from human error.
"As prime minister, I owe everyone, but most of all the relatives of the victims, an apology," he wrote on Facebook. "Justice will very fast investigate the tragedy and determine liabilities."
A station master in the nearby city of Larissa who was on duty at the time of the crash was charged this week with endangering lives and disrupting public transport.
The station master, who cannot be named under Greek law, appeared before a magistrate on Sunday after his lawyer requested extra time on Saturday to respond to the charges following new information concerning the case. Those proceedings were ongoing.
Railway workers' unions say safety systems throughout the rail network have been deficient for years as a remote surveillance and signalling system has not been delivered on time. They have called on the government to provide a timetable for the implementation of safety protocols.
Mitsotakis said on Sunday that if there had been a remote system in place throughout the rail network "it would have been, in practice, impossible for the accident to happen".
Greece would soon announce action, he said, adding that Athens would seek expertise from the European Commission and other countries on improving rail safety.
Pope Francis said on Sunday his thoughts were with the crash victims. "I pray for the dead, I am close to the injured and their relatives, and may Our Lady comfort them," he said in his weekly address to crowds in St. Peter's Square, Rome.
(Reporting by Alkis Konstantinidis and Stelios Misinas, Additional reporting by Angelo Amante in Rome; Writing by Angeliki Koutantou; Editing by Frances Kerry)