The Church of England said yesterday that police counter-terrorism operations were directed disproportionately against Muslims and risked alienating them.
In a submission to the Commons home affairs committee, the church's mission and public affairs council supported a proposed law against incitement to religious hatred, including towards Muslims, to preserve community relations.
The submission, signed by Dr Tom Butler, Bishop of Southwark, said: "In recent years stop and search powers have been employed disproportionately against Muslims...
"While this situation is not the same as that facing black communities in earlier times, confrontational methods of policing are likely to prove counter-productive, as they risk increasing radicalisation of young Muslims in particular.
"It can be argued that counter-terrorist operations directed against al-Qaida could be expected to affect the Muslim population disproportionately, but the scale of the disparity in a number of areas and the lack of objective justifications for it suggest that the explanation is unlikely to be reassuring.
"That Muslim communities experience counter-terrorist policy as discriminatory and threatening is a serious cause for concern."
All the churches have tried to show solidarity with local Muslims in recent years, the Archbishop of Canterbury, Dr Rowan Williams, taking the lead in fostering dialogue.
But Muslims reacted angrily when his predecessor, George Carey, who had himself fostered dialogue, argued earlier this year that their leaders should do more to condemn terrorism and that their faith was becoming associated with violence around the world.
Much more cautiously, yesterday's submission argued that the claim by al-Qaida that it was an Islamic organisation defending Islamic interests was the big threat to community relations.
"This [claim] may encourage misrepresentation by some people of Muslims ... as supportive of terrorism, and conversely misrepresentation of counter-terrorist measures as essentially anti-Islamic...
"Many in the Muslim community feel isolated, anxious and misunderstood within wider society as a result of the current situation."
It said that the powers of arrest under the Terrorism Act 2000 had been used disproportionately against Muslims, and the provisions of the following year's Anti-Terrorism Crime and Security Act had led to differential treatment of British and foreign nationals, the latter being liable to indefinite detention.
"[This] contributes powerfully to a sense of double standards of justice, liberty and dignity between British citizens and others, most of whom are Muslims, and indirectly to a sense of injustice ... new efforts should be made to frame legislation which deals with all terrorism regardless of the nationality of suspects."
The church called on the media to exercise restraint and not reinforce prejudices, adding: "It is very unfortunate that the opinions of a handful of unrepresentative extreme figures are regularly given prominence."
Good community relations required the unequal legal protection given to different religions to be rectified, though the church added that legislation should penalise religiously motivated incitement of harm but not robust argument in the criticism of religious beliefs and practices, even though some might find that offensive.