About 100,000 UK youngsters attend Islamic religious schools attached to mosques - madrasas - every day.
A new curriculum aims to tackle extremism and counter messages about perceived clashes between Islam and British culture.
It was drawn up by a group of mosques in Bradford and is being backed by the Communities Secretary Ruth Kelly.
Ms Kelly said: "We cannot afford to allow our young people to be intimidated and influenced by extremist messages.
"Madrasas have a pivotal role to play in winning hearts and minds and supporting young people to reject the messages of extremist groups.
"This project ensures that young Muslim students learn the true teachings of Islam and encourages them to play an active role in their local communities and as citizens.
"I would like to see citizenship on the curriculum of madrasas up and down the country, as this kind of grassroots action is key to facing down extremist messages."
Ms Kelly's department is working with Department for Education and Skills officials and representatives of supplementary schools to try to ensure good practice across the sector.
Although state-funded Muslim schools study citizenship as part of the national curriculum, madrasas are fully independent and ministers have no jurisdiction over what they teach.
Muslim children might attend a madrasa in the evenings after their normal school day or at the weekend.
The citizenship course itself, created by the Bradford Council for Mosques (BCFM) and known as the Nasiha project, aims to show that the spirit and teachings of the Koran are rooted in respect and tolerance.
It has been developed to promote community cohesion and help small communities be resilient to the small minority of extremists who promote violence and hate in the name of Islam.
The council said aspects of citizenship are already an integral part of teaching programmes in many mosques and madrasas in Bradford.
BCFM spokesman Sher Azam said Muslims wanted their children to be recognised as hard-working, active and proud people who cherished others.
He added: "We very much hope that teachers in mosques, madrasas and schools will use the resource pack as a teaching aid.
"Now that the document is in the public domain we will welcome feedback from practitioners and others in order to further develop and improve its contents."
The government says the course will teach students to value human life and reject violence as well as giving them practical skills to help them reject any extremism that may come their way.
It will encourage students to play an active part in local life through volunteering and community work and underline the importance of voting and taking part in the democratic process.
Imams and teachers will be provided with lesson plans designed to promote discussion and dialogue.
The government says five madrasas and one school in Bradford have already adopted the programme and 10 imams in the city have undergone training to teach citizenship.