Some 4,000 protesters, according to organisers, and 3,000, according to police, turned out close to the village of Saint Remy-de-Maurienne in southeastern France in defiance of an official ban on the gathering, an AFP correspondent said.
Police then deployed tear gas when a faction of protesters began to hurl projectiles at security forces.
At one point protesters blocked a main road.
Others stormed the nearby railway line, the AFP correspondent said, although train traffic had been halted due to the situation in the early afternoon, according to operator SNCF.
Interior Minister Gerald Darmanin said 12 police officers were injured in the clashes.
Protest organisers spoke of several injuries among their ranks.
Darmanin added that "96 foreign nationals known to the authorities were turned back at the border" and over 400 "dangerous objects" seized.
Five busloads of Italian activists -- around 280 passengers -- were held up at the border for several hours before being turned back, as people subject to administrative bans had been spotted on board, according to a local prefect.
One of those addressing the protesters, Pina of the Soulevements de la terre (Earth Uprisings) group said it was "scandalous... that the state and the government should decide to attack a movement, environmental activists, farmers and trade unions, when what we really need to do today is to attack all industries and all those who destroy living things".
Calm was restored in the evening.
Supported by the European Union, the new line should eventually link France's Lyon and Turin in Italy, with a 57.5-kilometre (36-mile) tunnel through the Alps.
The estimated cost is more than 26 billion euros (more than $28 billion).
Supporters say it will greatly ease freight road traffic but opponents say the ecological damage risks being devastating and that springs are already starting to dry up due to the works.
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