Ayrault said the incident was "very grave" and spoke of "unbearable violence" during a visit to the eastern city of Forbach, adding that "we must constantly fight against all forms of anti-Semitism, of racism, using firm measures, but also by educating people."
The attack took place on Saturday in Villurbanne near Lyon as the three victims, all of them wearing Jewish skullcaps, left a Jewish school in the east-central city, according to police.
A group of people jostled and insulted them, then about 10 other assailants armed with hammers and bars joined in, striking the victims.
One youth suffered a wound to the head and a girl was struck in the neck, according to authorities in Lyon. The third was hit on the arm.
Crif, the body which represents Jewish organisations in France, said it saw a direct link between Saturday's attack and the killing of three Jewish children and a teacher in Toulouse in March by a self-confessed Al-Qaeda follower.
"The link appears indisputable to me, as we have statistics," said Crif president Richard Prasquier. "In the weeks that followed (the Toulouse killings), there was a considerable increase in the number of anti-Semitic acts."
The National Bureau of Vigilance Against Anti-Semitism said the attackers in Saturday's incident were of North African origin.
The French Catholic Bishops Conference as well as the French Council of the Muslim Faith both condemned the attacks and assured the Jewish communisty of their "fraternal solidarity".
Investigations are under way but no suspects have yet been arrested.