Several hundred demonstrators, including around 50 who were masked and dressed in black, were involved in the confrontation, some throwing stones as gendarmes fired tear gas.
About a thousand activists had gathered at a chateau near the site of construction work on the A69 Toulouse-Castres motorway to show their opposition to the project.
The meeting went ahead despite having been banned by the local Tarn prefecture because of "serious violence" at previous protests. The manor house's owner had agreed to the gathering there, on condition it was peaceful.
Some protesters however used tree trunks, branches and wooden pallets to block the main road running alongside the A69 worksite, a route that had already been closed off to traffic.
AFP journalists saw them set bushes on fire, tear up a traffic sign and try to get on to the motorway site as they clashed with the gendarmes.
- 'Let nothing pass' -
Before the protest, Interior Minister Bruno Retailleau had warned on X that "we will let nothing pass".
He added: "When, in the name of ecology, dozens of ultra-left masked and dangerous activist protesters... who only want to destroy or attack cops, are mobilised, then we have shifted into sedition and ultra-violence."
The prefecture posted photos on X of items seized from the protesters, including axes, a pick and a crowbar.
Work on the motorway began in 2023 and is due to finish in the second half of 2026, but opponents still hope to stop it being finished.
In February, an administrative court in Toulouse ordered a halt to work on the project, ruling there was no major pressing public interest that justified the damage to the environment.
That ruling was hailed as a victory by the motorway's opponents.
But it triggered a number of initiatives by the project's backers, in particular a proposed law aimed at granting the required environmental approval retroactively.
That is expected to become law in the next few days, following a final parliamentary vote.
At the end of May, the Toulouse administrative court of appeal ruled that work on the motorway could continue ahead of a more detailed examination of the case set for the end of the year.
elr-ap/jj/jhb
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