Witnesses say police used pepper grenades and tear gas as well as flashballs, to try to control the situation.
There are unconfirmed reports of injuries.
“We were faced with very determined opponents, who have increased considerably in number over the weekend, following internet appeals. Security forces had to deal with violent projectile attacks and disperse groups of assailants using tear gas”, said a communiqué issued by the regional police.
The police intend to continue to dismantle the camps so that preliminary work clearing the undergrowth can begin.
Police began trying to evacuate the Le Sabot area, where the opposition to the camp first began. A group of about fifteen protestors remain on the roof at Le Sabot.
Around twenty tractors were ordered to turn back under threat of a charge by riot police, according to a passenger in one of the tractors.
Farmers are among those protesting against the construction of the airport, which is being built on protected swampland.
The project is financed partly by the state and partly by private investors, and the intention is to replace the current airport Nantes Atlantique, which is to the south of the city area.
Until he was appointed Prime Minister in June, Jean-Marc Ayrault was Mayor of Nantes.