It outlined plans to set up a "dialogue forum", tapping leading associations, intellectuals and other notable figures from the Muslim community for regular talks with the government.
Much of the focus will be on the training of Muslim preachers, trying to "encourage the emergence of a generation of imams fully engaged in the Republic", an interior ministry source said.
Radicalisation in prisons is also central to the reform efforts.
Two of the three Paris attackers are thought to have been radicalised in prison, where a chronic shortage of Muslim chaplains -- there are only 180 nationwide -- has often ceded spiritual guidance to extremists.
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Prison chaplains "will only be recruited if they have obtained the new training diploma in the fundamental principles of the Republic," Interior Minister Bernard Cazeneuve said.
The government is aware that it is treading on sensitive ground and is keen to avoid charges it is seeking to dictate religious practices, which would itself be a breach of the country's strict separation of church and state.
But it wants imams to take a new civic responsibility diploma, to be offered at a dozen universities by the end of the year, to imbue them with the values of a country that prides itself on liberty, equality and fraternity.
"Certain imams lack knowledge of the language and the law," the ministry official said.
It is a difficult balancing act for the government, and previous attempts to open a dialogue with Muslims have stumbled in the past.
A short-lived Islamic Foundation set up in 2005 was also considered a failure, but has been revived under the new reforms with the aim of providing training, research and cultural expertise.