In Paris, organisers said 12,000 students marched in protest, some clashing with riot police. Police said 4,000 students took part.
Student groups said at least 170 high schools across the country were disrupted or forced to close. Entrances to about 45 schools in the Paris region were at least partially blocked, police said.
The protests began yesterday after the high-profile deportation of a 15-year-old Roma girl, Leonarda Dibrani, and the expulsion of another 19-year-old student to Armenia on Saturday.
Sources in President Francois Hollande's government said it would make a statement about Dibrani at the weekend, after an investigation into how her expulsion was handled.
Valls said he would be given the results of the investigation on Saturday.
The Socialist government has raised the possibility of changing policy so that currently enrolled students cannot be expelled from France.
Much of the anger has focused on how Dibrani was forced to get off a bus full of classmates in the midst of a school outing before she was deported with the rest of her family to Kosovo.
At the Lycee Charlemagne secondary school in Paris's Marais district, rubbish bins were piled up in front of the entrance and a banner had been unfurled reading: "Charlemagne is mobilising for Leonarda and Khatchik".
"These are students just like us. They must absolutely be allowed to return to France," said one of the protesters, Heloise Hakimi.
"We are creating a movement that is growing in France to demand their return," she said.
Student groups said that as well as the Paris march, another 10,000 protesters took part in demonstrations in cities across France, including in Marseille, Grenoble and La Rochelle.
Education Minister Vincent Peillon has urged the students to return to classes and stop preventing other pupils from attending school.
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