Macron said he wanted to "free Islam in France from foreign influences" in a speech that critics said stigmatised Muslims.
French President Emmanuel Macron presented his plan to combat "Islamic separatism" on Friday, announcing his intention to "free Islam in France from foreign influences".
He said the country would end a system allowing Imams to train overseas and would take control of religious funding.
"The goal of training and promoting in France a generation of Imams and intellectuals who defend an Islam fully compatible with the values of the Republic is a necessity," Macron told an audience in Les Mureaux, a city located in Paris' suburbs.
Macron added that the certifying of Imams in the country will change with the French Council of the Muslim Religion formalising their training.
Many of France's Imams come from countries such as Turkey, Morocco and Algeria. Macron spoke previously on the topic in February.
The speech comes a week after a stabbing in Paris outside the former headquarters of satirical magazine Charlie Hebdo that reignited a national conversation about terrorism.
Gérald Darmanin, Macron's new interior minister, who watched on during his speech, said last week that France was "at war against Islamic terrorism".
But several French parliamentarians said that Macron was stigmatising Muslims and speaking of one societal division instead of the many that exist.
Manon Aubry, a left-wing member of the European Parliament, said the president spoke about Islam "obsessively."
"Stigmatising Muslims, this is his only solution to try to hide his calamitous management of the health and social crisis," Aubry tweeted.
Alexis Corbière, a French MP from the same left-wing party La France Insoumise, said Macron had only talked about radical Islam instead of focussing on an increasing gap between rich and poor and other societal divisions that, he said, influences "separatism" in poorer communities.
Meanwhile, right-leaning politicians said Macron did not go far enough.
"Few strong and courageous measures...The refusal to ban the veil for accompanying people on a school trip is a mistake. Nothing on immigration," tweeted Eric Ciotti, an MP from the Republicans party.
Among the other measures that will be introduced is a requirement from age three for children to go to school, with heavy limits on homeschooling.
"Every month, prefectures close illegal schools, often administered by religious extremists," Macron said.