Speaking outside Paris on Friday, Mr Macron said "Islamist separatism" was a danger to France because it held its own laws above all others and "often results in the creation of a counter-society".
He said this form of sectarianism often translated into children being kept out of school, and the use of sporting, cultural and other community activities as a "pretext to teach principles that do not conform to the laws of the republic".
"Islam is a religion that is in crisis all over the world today, we are not just seeing this in our country."
The measures announced by the president will form legislation that will go to parliament before the end of the year.
They include: stricter monitoring of sports organisations and other associations so that they do not become a front for Islamist teaching an end to the system of imams being sent to France from abroad improved oversight of the financing of mosques home-schooling restricted
Mr Macron also said France must do more to offer economic and social mobility to immigrant communities, adding that radicals had often filled the vacuum.
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"History Is Much Like An Endless Waltz. The Three Beats Of War, Peace And Revolution Continue On Forever." - Gundam Wing: Endless Waltz