There were clashes between police and protesters on Friday, with teargas being fired, barricades being erected and at least four people arrested.
Ten gendarmes were injured in an ambush on Thursday, according to police.
One was reportedly hit by acid and two by stones or Molotov cocktails.
The protesters deny the ambush claim.
Macron government scraps airport plan
Environmental protesters and farmers have occupied the Notre Dame des Landes site since the previous government revived a longstanding plan to build an airport there.
Since then there have been numerous demonstrations and clashes with police in the area.After commissioning a report on the airport project last year, the government announced it would be scrapped in January.
But Prime Minister Edouard Philippe swore that the occupation would be ended, calling it a "lawless zone", and 2,500 gendarmes and bailiffs moved in this week to clear the area.
On Thursday they declared their mission accomplished but said they would remain in the area to ensure that roads were open to motorists.
Police, protesters injured
The police, who claim "extremely violent, ultraleft" outsiders flocked to the site during the week, say that dozens of officers have been injured since Monday, while medical teams say 110-120 protesters have been injured.
A number of collectively run farms have been destroyed, the Mediapart website reports.
An investigation is taking place at one farm after a rocket was fired at a police helicopter three days ago.
In a television interview on Thursday, President Emmanuel Macron said that "everything that can be evacuated has been evacuated", announcing an effective truce to "allow the legal farming projects to go ahead".
The representative of central government in the area, Nicole Klein, on Friday called on campaigners who want to stay to register a plan to farm there within the next 10 days, explaining that she had ordered a simplified version of the necessary paperwork to be made available.
Klein said she hoped to meet a delegation of protesters "as soon as possible".
A court in Nantes on Friday threw out an appeal by Cédric Dussant, who worked on one of the farms, against his expulsion.
A demonstration is planned at the site on Sunday.