Athens is planning to modernise the area where the camp is located and relocate the occupants.
Clashes broke out near Athens after Greek riot police moved to evacuate one of the last refugee camps in the capital.
Authorities attempted to empty the Eleonas camp early on Thursday morning to evict around 670 people who live there.
Images from the scene show migrants and activists setting up barricades before clashing with police, who used tear gas to force some people back.
According to the NGO Solidarity With Migrants, only around 30 people were evicted in the operation.
"In cooperation with the municipality of Athens, we are proceeding with the closure of the Eleonas camp, as the modernisation of the area progresses and there are places available in other existing structures," Greek Migration Minister Notis Mitarachi wrote on Twitter.
"Unfortunately, a small number of migrants and groups that support them are trying to undermine the movement."
The Eleonas refugee camp was the first to open in mainland Greece in August 2015 and has been visited by several world leaders.
Officials are hoping to evict the remaining occupants by the end of the year and relocate them to Schisto, the last remaining camp in Athens.
Greece has denied frequent allegations by NGOs that it has illegally pushed back asylum seekers.
Solidarity With Migrants says that migrants have only consented to be transferred from Eleonas after "many threats and lies from the camp management".
The NGO says that many do not want to move until Greek authorities secure housing for them in the city.