An arson attack also damaged a Citibank branch in another part of the capital before dawn on Tuesday.
The central Athens attack on the newspaper occurred late Monday, and left the windows of the office block entrance smashed and walls splashed with red paint.
Leaflets scattered by the hooded youths said the attack was a response to media coverage of recent violence by anarchist gangs. The incident lasted a few minutes and no arrests were made.
Government, opposition party and media union officials all condemned the attack.
"This is an attack against the press and press freedom," government spokesman Evangelos Antonaros said shortly after the attack, standing outside the newspaper's offices.
Violence by Greek anarchist groups has spiked in recent weeks, with arson attacks against police stations, banks and traffic surveillance cameras.
Separately, a branch of Citibank was damaged in an arson attack in a northern area of the capital.
No one was hurt when small cooking gas canisters exploded outside the entrance of the bank in the Agia Paraskevi area of the city.
Residents of an overlooking apartment block were evacuated until the fire was put out. So far, no one has claimed responsibility for that attack.
By: Several dozen youths carrying sledgehammers, steel bars and bricks attacked the offices of the daily Apoyevmatini newspaper, damaging the entrance but causing no injuries, police said Tuesday.