A riot at the Koyrdallos prison, in a western suburb of the city, began after several hundred protesters started throwing rocks and other missiles at police, a prison guard said.
The police responded by firing tear gas at the protesters.
While the guard said the prison was "calm", demonstrators were refusing to leave the scene and were staging a sit-in.
In the northern city of Thessaloniki, more than 1,000 demonstrators marched to protest against the shooting of Alexandros Grigoropoulos.
The protesters, for the most part associated with left-wing radicals, set off without incident from the city centre at around 1600 GMT.
Nicole Itano, Al Jazeera's correspondent in Athens, said: "There is still lingering tension in the air. We still see very strong resistance from universities. We were just at the polytechnic university in Athens... and there are masked men outside checking, stopping people from going inside.
"That area of the city still looks very much almost like a warzone, you see burnt stores and cars in the area, the police don't even dare to go in there to clean things up.
"The storm is still not completely past, there is still the potential for more trouble in the days to come."
The new clashes come a day after the arrest of a Greek police officer charged with the premeditated manslaughter of Grigoropoulos and illegal use of a weapon.
The killing of Grigoropoulos has touched a raw nerve among young Greeks, angry at years of political scandals and rising levels of poverty and unemployment, worsened by the global economic downturn.
|Epaminondas Korkoneas, centre, is escorted to the office of Athens' prosecutor [AFP]
On Wednesday, an Athens court indicted Epaminondas Korkoneas for the death of Grigoropoulos, while charging his colleague Vassilios Saraliotis as an accomplice to the crime.
Both men were ordered to be held in jail pending their trial, which has no set date as yet. The two policemen have been suspended from their duties.
But Korkoneas' defence lawyers said on Wednesday that the bullet that killed Grigoropoulos had ricocheted and accidentally hit him, rather than being a direct shot.
On Wednesday, groups of youths threw petrol bombs near the country's parliament and riot police fired tear gas to disperse crowds as more than 10,000 people marched as part of a labour strike through the city's centre.
The national strike - planned weeks before the riots broke out - had paralysed much of the country's infrastructure, closing down schools, public services and hospitals and grounding flights.