Access to the Hellenikon airport site was blocked off in the morning, and dozens of police officers and riot police stood by as the roughly 600 migrants collected their belongings and boarded buses to refugee camps elsewhere in Greece.
Police said about 350 people, mainly families, would go to a camp in Thebes, about 70 kilometres northwest of Athens, while the remainder of mainly single people would go to Derveni, about 140 kilometres west of the capital.
Migrants and Greek activists have held several demonstrations at Hellenikon to protest living conditions there over the past few months.
The site, which includes Athens' old international airport and 2004 Olympic Games venues, is part of Greece's privatisation efforts and is slated for a massive seaside urban redevelopment project worth an expected 7 billion euros ($7.8 billion).
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The Hellenikon complex, largely abandoned over the last 13 years despite the country's deep financial crisis, had been used to house up to 3,000 migrants. Most had been living in tents and in poor conditions inside the buildings during their stay.
The Hellenikon development is led by Greece's Lamda Group with a consortium of overseas investors, and is planned to include a large park, shopping and recreation areas and hotels.