Officers fired rubber bullets as demonstrators hurled bottles of acid in the western city of Nantes.
Protesters also clashed with police in the southwestern city of Toulouse.
The demonstrators were protesting over the death of Remi Fraisse, 21, who was killed last Sunday during clashes between security forces and protesters at the site of a contested dam in southwestern France.
Initial investigations showed traces of TNT on his clothes and skin, suggesting he may have been killed by a police stun grenade.
Many who took part on Saturday's protests, which also took place in other cities including Lille, Bordeaux and Avignon, were said to be opponents of the controversial dam project.
French Prime Minister Manuel Valls condemned the violence, saying it was an "insult to the memory" of Fraisse.
Fraisse's death was the first during a protest in mainland France since 1986.
Overnight Thursday, some 200 protesters rampaged through the western city of Rennes, with some turning over cars and breaking shop windows.
It was "impossible" in light of the tragedy to "continue any work on the site" of the Sivens dam project in the Tarn region, said Thierry Carcenac, head of the Tarn's executive council.
Ecology Minister Segolene Royal will next week gather together all warring parties to discuss the future of the Sivens dam.
Opponents of the project say the dam will destroy a reservoir of biodiversity and will benefit only a small number of farmers.
Those promoting the dam say it is in the public interest by providing irrigation and aiding the cultivation of high-value crops.
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