Demonstrators threw missiles at officers who have been blocking access to woodland at the Bure plant, halfway between Paris and Strasbourg, since a protest camp was dismantled 10 days ago.
Lejuc wood was selected by France's radioactive waste agency (ANDRA) for exploratory drilling ahead of an application to create a nuclear waste storage site.
Police evacuated the forest of about 15 protesters during a major operation on 22 February.
Saturday's rally began calmly with a march of about 300 people, according to police, as demonstrators held meetings and debates.
But during the afternoon a group of protesters, many wearing masks, headed for Lejuc wood, where scuffles broke out with police.
Bure was chosen in 1998 to house a laboratory, 500 meters underground, in preparation for the burial of the most radioactive or long-lasting nuclear waste in France. As yet, no radioactive waste is on the site.