More than 4,000 people rallied outside the Greek parliament for a third time this month to oppose mandatory inoculations for some workers, such as healthcare and nursing staff.
A police official, who asked not to be named, said some protesters had thrown petrol bombs, prompting the police to respond with tear gas.
A rally on Wednesday was also marred by violence.
Recent polls showed the majority of Greeks would get the shot against the COVID-19 which has claimed 12,890 lives in Greece since the pandemic broke out last year. About 45% of a population of 11 million are fully vaccinated.
Greece has ordered the vaccination of healthcare and nursing home staff as cases have risen and urged school teachers to get the shot in time for the start of the school year in September.
Nearly 2,500 cases were reported on Saturday, bringing the total number of infected people to 474,366.