Over 300 protesters joined the demonstration - some helmeted and wielding stones, sticks and shields, according to the authorities.
Officials say demonstrators threw stones and at least one Molotov cocktail at police who responded with water cannon, tear gas and stun grenades.
According to calls to the emergency services published by the police, three demonstrators were injured.
But organisers say six were seriously injured and about 30 suffered slight injury.
The rally was one of a series of demonstrations to oppose plans to store highly radioactive waste - the dangerous long-term byproduct of France's extensive nuclear energy programme - 500 metres underground at a nearby site.
Minister hesitates to take stand
Earlier this month, the Nuclear Safety Authority said it had "reservations" about the project, known as Cigéo, notably because of the potential danger from highly inflammable material in the case of rising temperatures.
And the body in charge of bulding the site has siad it will not be opening before 2022, with its boss, Pierre-Marie Abadie, expressing concern at the rising tension around the site.
France's Environment Minister Nicolas Hulot has said he needs more information before he gave his position on the project.
However, the site's opponents recently published a photograph of him back in October 2016, before he became minister, brandishing a placard reading "Cigéo, I say no!"