The charter offers "a clarification of how the Muslim community is organised," Macron said after a meeting with representatives of the French Council of the Muslim Faith (CFCM), his office said.
It will also provide a framework for a new National Council of Imams that will be responsible for vetting imams practising in the country.
"This is a clear, decisive and precise commitment in favour of the republic," Macron said, hailing "a truly foundational text for relations between the state and Islam in France."
Macron had urged the council to act against "political Islam" in November after the killing of Samuel Paty, a teacher who was beheaded outside his school after showing controversial cartoons of the Prophet Mohamed as part of a free-speech lesson.
The attack prompted a crackdown against extremist mosques and Islamist associations, along with a vigorous defence of French secularism.
'Defending foreign regimes'
The new 10-point charter "states clearly that the principles of the Muslim faith are perfectly compatible with the principles of the republic," CFCM president Mohammed Moussaoui told journalists after the meeting.
READ ALSO: French Muslim groups draw up charter to reject 'political Islam
The accord was hammered out Saturday during a meeting with Interior Minister Gérald Darmanin after weeks of resistance from some CFCM members who objected to a "restructuring" of Islam to make it compatible with French law and values.
Moussaoui said all eight of the CFCM's federations, representing various strands of Islam, approved the charter, but three had yet to sign the accord because "they need a bit more time to explain what it means to their followers," an Elysée official said.
Hakim El Karoui, an author and expert on Islam in France, called the intention of the charter "praiseworthy", but said it also shone a harsh light on internal tensions at the CFCM which he said consists of "five federations financed by foreign countries and three federations that are Islamist".
El Karoui said "the charter was adopted by people whose interests clash with the text".
Franck Fregosi, an Islam expert at research institute CNRS, said no other country, and no other religion in France, had a comparable charter.
"I'm not certain that this text, even once it gets signed, will get wide backing from Islam on the ground," he said.
Back-to-front?
The imam of the mosque in the southwestern city of Bordeaux, Tariq Oubrou, said the charter had been developed back-to-front.
"It should be Muslim scholars and theologians who write a text and then submit it to the CFCM, not the other way around," he said.
The charter rejects "instrumentalising" Islam for political ends and affirms equality between men and women, while denouncing practices such as female circumcision, forced marriages and "virginity certificates" for brides.
"No religious conviction whatsoever can be invoked as an exemption from the duties of citizens," it states.
It also explicitly rejects racism and anti-Semitism, and warns that mosques "are not created for the spreading of nationalist speech defending foreign regimes".
Macron has also said that authorities plan to expel the roughly 300 imams in France sent to teach from Turkey, Morocco and Algeria.
The charter accord comes as a parliamentary commission began debate Monday over a new draft law to fight "pernicious" Islamist radicalism with measures to ensure France's strict separation of religious bodies and state in the public sphere.
The legislation would tighten rules on issues from religious-based education to polygamy, though Macron has insisted the goal is to protect all French citizens without stigmatising the country's estimated four to five million Muslims, the largest number in Europe.
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