Thunberg is expected as part of an international delegation on Saturday at the site near the southwestern city of Toulouse, protest organisers the Cabanade group.
A global figure in the fight against climate change, Thunberg has been fined by one Swedish court for her direct action protests there.
But she saw another case against her thrown by an English court last week.
On Friday, French police fired tear gas and made arrests at the site in Saix where a new motorway is planned, AFP journalists on the scene saw.
"It seems like (police) want to disrupt in advance" the planned event which includes workshops, discussion groups and concerts, the organisers said in a statement.
Cabanade had gone ahead with setting up the protest despite authorities banning the gathering because of "risks of serious harm to public order".
AFP journalists saw at least two arrests and the use of tear gas by police at the site.
- Police clear barricades -
Activists had set up camp toilets and signposts on private land where they planned to create a so-called "zone to be defended".
Police cleared pallets and trolleys used to block a small road running alongside the field, which is close to the route of the planned A69 motorway linking Toulouse and the town of Castres.
"The operation by 102 police allowed the clearing of booby-trapped barricades, seizure of material planned to be used to build treehouses and to restore order," the local prefecture said in a statement.
Activists said around 100 people on site were "resisting", in posts on the Telegram messaging service.
Other messages appealed for help and materials to build treehouses in a wood protesters hope to protect.
Police had carried out a "brutal" intervention using rubber bullets and stun grenades, said Bernard, a white-haired demonstrator wearing overalls.
AFP journalists could not immediately confirm the use of controversial riot control weapons, which have inflicted serious injuries in France in the past.
"I always hold peaceful meetings with peaceful people," said Greens MP Christine Arrighi, who planned to attend the weekend event.
"You'd think we were in Minority Report," she added, referencing the 2002 Steven Spielberg movie in which police arrest people before they have committed any crime.
A police source told AFP they expect up to 200 people to attend the protest, while organisers estimated between 500 and 1,000.
"We're going ahead with the event, because it's a private event on private land," said Paul, a spokesman for the movement who asked not to give his family name.
He added that the wooded area is the subject of a dispute over its expropriation for the motorway.
Environmentalists have protests several times in recent months along the planned route of the A69.
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