The evacuation had started at 0600 Paris time (12 a.m. ET), the French interior ministry said, Reuters reported.
In January, President Emmanuel Macron's government dropped plans for the 580-million-euro ($712-million) airport in Notre-Dame-des-Landes in western France, a sensitive decision that past governments had shirked for decades.
Supporters of Notre-Dame-Des-Landes, designed to handle 4 million passengers a year initially, said it would aid economic development in the Loire-Atlantique region.
They argued an old, inner-city airport 30 km (19 miles) to the south was congested and a security risk.
But opponents said it was too costly, environmentally unfriendly and that there was another under-utilized airport 110 km (68 miles) to the north, near Rennes in Brittany.
Construction giant Vinci has said it is ready to discuss government compensation for loss of its earlier contract to develop Notre-Dame-des-Landes.