Some protesters took aim at the US administration of Donald Trump and others carrying Palestinian flags.
The rallies took place amid the rightward shift in French politics, with the government pledging to tighten immigration policies and border controls.
Two people were arrested and three people injured, including a riot police officer, during the clashes in Paris, the ministry statement added.
Many of those marching highlighted the growing strength of reactionary political forces, in France but also in the United States.
“Fascism is gangrene from Washington to Paris,“ read one placard.
“It’s scary because in France we see far-right ideas becoming more and more commonplace, even among ministers in this government.”
One American protester said similar demonstrations should be taking place in the United States.
Aurelie Trouve, a lawmaker for the hard-left France Unbowed (LFI) party, pointed to the growing popularity of the far-right party of Marine Le Pen in France.
In the southern port city of Marseille, some 3,300 people took to the streets, while 2,600 protested in Lille in the north, according to police.
Ines Frehaut, a student taking part in her first demonstration, said some of the statements from France's hardline interior minister worried her.
The protests took place a day after the International Day for the Elimination of Racial Discrimination.
“There is a global reactionary offensive against foreigners and their children, against Muslims,“ added Dominique Sopo, head of SOS Racisme, also pointing to increasing racist and anti-Semitic acts.
The image pictured Hanouna, who was born into a Jewish family that had immigrated to France from Tunisia.
Critics accused the LFI of imitating the anti-Semitic tropes of the Third Reich. Key LFI figures admitted publishing the image was a “mistake” and it was withdrawn.
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