The start of citizenship classes in mosques for thousands of young British Muslims is the result of a concerted effort by the British Government to prevent a new generation being indoctrinated by extremists.

Hazel Blears, the Communities Secretary, announced today that trials of the new lessons will begin in several big cities with large Muslims populations at the start of the school year in September. The aim, she said, is to build an alliance against extremists and to make sure that young Muslims recognise that their faith teaches shared citizenship values. The classes, to be held alongside traditional lessons about the Koran, are to show young people "that their faith is compatible with shared values and with being a British citizen."

Significantly, senior Muslims in Britain have welcomed this step. Sheikh Ibrahim Mogra, an imam with the Muslim Council of Britain, said the initiative for this had come from the Muslim community itself, and was not something imposed on them by the Government. "We feel our children need to be taught that they can be proud Muslims and proud young British people," he said in a radio interview today. The Government supported the scheme, he said, but the Government had been told that it should not interfere in Islamic theology or the way young Muslims were trained.

The initiative, however, is a clear vindication of the Government's determination to halt the alienation of young Muslims and curb the influence of radical imams. Soon after the bombings in London in July 2005, Tony Blair, then Prime Minister, announced 64 measures aimed at increasing supervision of what was being taught in mosques. He said foreign imams who could not speak English would not be given visas to enter Britain; bookshops and mosques selling extremist literature would be closed; extremists would be deported; and working groups would be set up with Muslim organisations to discuss travelling "roadshows" to stage debates in city centres where young people could engage with moderates.

Many Muslims at the time were angered, believing they were being targeted. They resented what they saw as government attempts to control their religion, and they accused Labour of ignoring a key factor in stirring Muslim anger - British foreign policy in Iraq, the Middle East and Afghanistan.

However, the Muslim Council of Britain, an umbrella organisation that includes many of the mosques and associations serving Britain's 1.8 million Muslims, set up its own study to look at how imams should be trained and how Muslims should reach out to non-Muslims around them. This study reported almost two years ago, and strongly endorsed the proper training of imams, the use of English to preach to young people, the setting up of inter-faith groups and the concept of citizenship education.

Meanwhile, the Government has become increasingly concerned that the concepts of citizenship and its rights and duties are not being properly taught in schools. Gordon Brown, the Prime Minister, has been keen to promote the theme of "Britishness" to prevent national fragmentation and to promote common values, loyalties and ideals. This theme is aimed not just at Muslims but at all ethnic minorities and would-be immigrants to Britain. It is also meant to be taught to native Britons to bolster patriotism and common values.

The issue has become controversial, especially as it has proved hard to define Britishness or to devise tests of what newcomers should know of British life.

But the idea of citizenship classes has nevertheless been broadly accepted. Part of the aim of the classes announced today is to isolate preachers who say that Islam is incompatible with democracy and Western values or that Muslims do not have any duty of loyalty of a Western state and government. It is important that these classes are to be held in mosques, where many young Muslims go at weekends for Arabic and Koranic lessons. In this way, the classes are set firmly in a Muslim context and do not appear to be forced on Muslims by a secular state.

The announcement comes as Britain's Muslim community is itself torn by debate over the place of religion in modern society and whether attempts to "modernise" Islam are legitimate. Lively debates are being held daily on the concept of "ijtihad" - the judicious interpretation of the Koran - and on the traditional pillars of belief.

One difficulty is that Britain's Muslims, unlike those in France or Germany, come from very diverse backgrounds. Some 40 per cent are of Pakistani origin, but there are substantial numbers also from Bangladesh, India, Somalia, the Arab world and Nigeria. All have different ethnic roots and religious traditions. There is therefore no unified Muslim leadership in Britain, nor any agreed school of Islamic studies.

Leading British Muslims, who have achieved positions in British society, have insisted that only if British Muslims can break out of their narrow ethnic or sectarian backgrounds will they have a chance to compete for jobs and influence in wider British society. They agree that fluency in English and an understanding of how British society works are essential prerequisites. The classes announced today are clearly intended to help them do this.