The raids came a day after tens of thousands of people took part in rallies countrywide to honor slain teacher Samuel Paty.
Gerald Darmanin said the swoop on militant networks was designed to send a message that "enemies of the Republic" would not enjoy "a minute's respite".
He said over 80 investigations had been launched for online hate speech following the attack, which has drawn parallels with the 2015 massacre at Charlie Hebdo satirical magazine, where 12 people were gunned down for publishing offensive cartoons of Prophet Muhammad (PBUH).
That attack -- the first in a string of assaults that have killed over 240 people in France -- brought over a million people onto the streets of Paris to denounce extremism.
On Sunday, people again congregated on Place de la Republique in Paris, where world leaders had marched alongside the French in 2015.
Some in the crowd chanted "I am Samuel", echoing the 2015 "I am Charlie" rallying call by supporters of “free speech”.
Paty, 47, was murdered on his way home from the school where he taught in a suburb northwest of Paris Friday afternoon.
A photo of the teacher and a message confessing to his murder was found on the mobile phone of his killer, an 18-year-old Chechen man Abdullakh Anzorov, who was shot dead by police.
Eleven people are being held over the attack, including a known militant and the father of one of Paty's pupils who had railed against him online and called for his dismissal.
Darmanin accused the two men of having issued a "fatwa" against Paty.
"They apparently launched a fatwa against the teacher," the minister told Europe 1 radio, AFP reported.
Anzorov's family arrived in France when he was six from the predominantly Muslim Russian republic of Chechnya.
Four members of his family, which sought asylum in France, are being held for questioning.
Paty had been the target of online threats for showing the offensive cartoons to his civics class.