Police fired tear gas and water cannons to disperse violent groups on the fringes of marches in Paris, Strasbourg, Rennes and Toulouse, among other cities overnight.
The marches drew more than 250,000 people in dozens of cities, the interior ministry said, though organisers said 450,000 had participated.
The protests, in which a teenager lost a hand on Monday, were the latest manifestation of public anger in a country where support for populist parties on the far right and far left has surged ahead of a presidential election in the spring.
The government is under pressure to tame public debt amid weak growth, and has struggled with basic tasks such as passing a budget since President Emmanuel Macron's allies lost their majority in a 2024 parliamentary vote.
Prime Minister Sebastien Lecornu told lawmakers at least 215 teenagers and 85 school staff had so far been injured in clashes, "the heaviest toll in decades paid by the school system". His office said more than 700 police were also hurt.
Macron has convened Lecornu and other senior ministers at an emergency meeting on Tuesday, broadcaster BFM reported.
The students' demands do not concern religion or immigration, but focus instead on understaffing and lack of funding. Marine Le Pen's far-right National Rally party has not linked the protests to France's migration policy. Lecornu's office did not respond to a request for comment.
In Marseille and Nantes, protesters held up handmade signs bearing phrases such as "The state has killed national education". In Toulouse, parents linked arms at the front of a march through the city.
Paris police said clashes in the capital resulted from some 300 people, most hooded or masked, facing off against security forces, and that the protest generally unfolded without major incident elsewhere. Several storefronts were damaged.
The Interior Ministry said 488 people had been arrested and 48 security personnel were injured on Tuesday.
The student protests began in September in the deprived suburbs of Paris before spreading nationwide.
Students complain about schools facing basic maintenance problems, from water leaks to rat infestations.
Rights groups, students and parent groups have accused authorities of using disproportionate force against minors. The government says the protest movement has been hijacked by outsiders and in some places deteriorated into urban violence.
More than 1800 people are being prosecuted for unspecified crimes, including 1483 minors, the justice ministry said on Monday.
Lecornu has ordered his ministers to tackle the students' leading demands. Those include ensuring absent teachers are replaced, reviewing the length of the 8am to 6pm school day and the need for longer lunch breaks.
French spending on education has lagged inflation and the country's students are trailing their OECD peers in overall performance, data from the PISA 2025 assessment shows.
