Police fired teargas at a group of about 300 people on the site at Notre Dame des Landes, near Nantes, at about 11.00am on Sunday.
"A group of violent opponents", according to a gendarmes' statement, had pelted them with stones, bottles, rockets and Molotov cocktails after being prevented from trying to reconstruct shelters that had been destroyed by a clearance operation during the week.
Two people were arrested in the morning, according to police.
Several thousand people rallied at the site in the afternoon for a peaceful demonstration of support for the campaigners who occupied the site for several years.
After a four-day operation to clear the area and open roads to traffic, the government on Friday invited squatters to submit plans to farm at the site for official approval, a move that right-wing MP Eric Ciotti on Sunday denounced as a "retreat in the face of violence".
Arrests in Montpellier
There was violence after a demonstration in support of the airport protesters in Nantes on Saturday, with shop windows and steet furniture smashed.
And 43 people were in detention in Montpellier, where the university has been occupied in protest at education reform plans since mid-February, on Sunday after clashes with police during a demonstration that sought to bring together opponents to the government's social policy.
The 51 arrests that took place on Saturday were an "obstruction of the right to demonstrate", according to the local branch of the Human Rights League.
The people detained, two of whom were from the organisation's legal team, were arrested two hours after the clashes and two kilometres away from the scene, the league's local president Sophie Mazas told the AFP news agency.
Left unity in Marseille
No clashes were reported at a larger demonstration - 6,000 according to the police, 58,000 according to the organisers - in Marseille on Saturday.
Hard-left leader Jean-Luc Mélenchon called for the "partition" between unions and political activists fighting President Emmanuel Macron's social policies at the demonstration, which brought together left-wing activists, many from his France Unbowed party, and trade unionists from the radical CGT and Sud unions.
After another two days of a rolling rail strike on Friday and Saturday, an opinion poll found 46 percent of those asked finding the strike justified and 61 percent wanting the government to see its reform on the rail network through to the end.