Clashes broke out in Athens during a general strike called across Greece in response to a rail disaster last month.
Protesters threw petrol bombs at a police cordon near parliament, while the walkout grounded flights and extensively disrupted service.
Riot police responded with tear gas and stun grenades during the brief flare-up of violence that disrupted peaceful demonstrations.
Large protests were also held in other cities across the country.
The demonstrations come after the head-on collision of a passenger train with more than 350 people on board with a freight train last month. 57 people were killed.
Clashes between protesters and police also erupted in the southern port city of Patras.
The strike has left ferries to Greek islands in port, left hospitals running with emergency staff, halted public transport services and led to class cancellations at state-run schools.
The strikes have been called in solidarity with the railway workers’ unions since the fatal rail crash on February 28.
“This government has had four years to fix problems with the rail network, but instead of owning up to that responsibility, they are blaming everyone else,” Popi Tsapanidou, a spokeswoman for main leftist opposition party Syriza, said.
The main protests were held in Thessaloniki, Greece's second-largest city, alongside demos in the capital, where thousands chanted “this crime will not be forgotten".
Stores and banks lowered their shutters when the protesters filed past as Athens was brought to a standstill.
The government, which faces a parliamentary election before the summer, says rail services will restart on March 22 and will be restored gradually until April 11, with additional staff to monitor safety.
Prime Minister Kyriakos Mitsotakis's centre-right government has seen a strong lead in opinion polls reduced in recent weeks over Syriza, with the two sides also locked in a debate over how to reform Greece's rail network.
Mr Mitsotakis has promised clearer boundaries between privatised services and the authorities overseeing them, seeking assistance from European Union experts in drawing up the changes.
But his political opponents argue that the poorly managed dismantling of agencies under state control has compromised rail safety.
