Tear gas clouded the streets in the eastern city of Strasbourg on Friday, fireworks were aimed at police lines in Marseille in the south and rubbish bins set ablaze in Rennes in the west.
In Paris, where there were also skirmishes, students waved placards reading "We have a future to build, not to endure".
Six months before the 2027 presidential election, opinion polls consistently show the deep unpopularity of Macron and his centre-right-leaning government.
Planned budget cuts, which exacerbate the funding crisis in education, have fuelled the discontent.
The protests erupted in the Paris region last week but have turned increasingly violent as they spread nationwide.
Justice Minister Gerald Darmanin told RTL radio that police had arrested 2000 people, most of them teenagers, since the protests began.
He said parents of those inflicting damage to property should be made to pay reparations.
Four hundred high schools - roughly 1 in 10 - were closed on Friday due to the unrest and Education Minister Edouard Geffray urged parents to dissuade their children from protesting in the streets.
"In the streets, the children are in danger," Geffray told BFM TV.
Darmanin said the student protest movement had been hijacked by "outsiders".
Students blockading their high schools have voiced anger over overcrowding in classrooms, regular shortages of teachers and dilapidated buildings, blaming years of underinvestment.
"We are 35 per class, we don't have enough chairs in classrooms, the one-hour lunch break (is too short) for everyone to get food," 15-year-old Kesia told Reuters in the Paris suburb of Pantin before running off as the police used tear gas.
Under the draft 2027 budget presented by the government on Thursday, the education budget is set to increase by a below-inflation 1.7 per cent to 65.53 billion euros ($A106 billion), excluding teacher pensions.
Education is traditionally the largest budget item, but that changes in 2027 with debt servicing costs expected to reach 74.5 billion euros, according to the draft bill.
Intelligence agencies told a crisis meeting on Thursday that the protest movement had been initiated by politicians from the hard-left France Unbowed party (LFI).
Senior LFI MPs rebutted the allegations and accused the government of politicising the protests.
Students and rights groups have accused the police of using heavy-handed tactics against minors, including the use of batons, tear gas and non-lethal flash-ball guns.
The interior ministry on Friday said it had opened three investigations into police violence against protesters.
In a sign the protests might spread beyond French borders, some high school students in the city of Liege, in Belgium, began protesting on Thursday.
A city hall spokesperson said high schools were closed on Friday.
