Dozens of far-right activists and local residents threw eggs and taunted hundreds of Muslim immigrants as they gathered to pray in a central square for Eid al-Adha surrounded by a protective cordon of riot police.
Greece, which has become the main immigrant gateway to the European Union, has a growing Muslim community and tensions between locals and incomers have run high in some Athens areas such as Attiki square, the scene of Tuesday's incident.
Athens' Muslim community is without an official mosque and prayers are usually held at cultural centers or community halls or private apartments around the city. The Muslim community in Greece is estimated at about 1 million, in a country where most people are Greek Orthodox Christians.
While the Muslims prayed, some locals shouted obscenities from their balconies and waved Greek flags. Leaflets that depicted pigs -- an animal Muslims consider unclean -- were scattered across the square.
"There is a (unofficial) mosque near here but we're afraid to go there," said a 30-year old migrant from Bangladesh, who gave his name as Shamasul. "Sometimes Greeks in the neighborhood threaten to kill us."
Margarita Vassilatou, 56, who has lived in the square for more than 35 years said she wanted to leave as a result of the immigrants:
"This is not a life ... We are afraid of them. Many of them are criminals, they carry knifes and deal drugs."
In another, more central square in front of Athens university, about 2,000 Muslim men and women prayed peacefully in front of the neo-classical university and ancient Greek statues.
In the past, moves to build a mosque in the capital have been met with opposition from local residents and some priests of the Greek orthodox church.
However, the current archbishop supports the construction of a mosque and the socialist government has set aside a site close to the city center, although building has not yet begun.
The only mosques in Greece are in the northeastern region of Xanthi near the Turkish border, home to a large Muslim minority.