The study by the International Helsinki Federation for Human Rights (IHF) covers 11 EU members states.
It looks at “widespread” negative attitudes towards Muslims, including unbalanced media reporting which depict Muslims as “an enemy within”.
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The report, “Intolerance and Discrimination against Muslims in the EU”, is based on second-hand accounts.
They include statements by Muslim and anti-racist groups, human rights organisations material, media reports and official documents.
In France, the debate over the French law forbidding religious clothing in schools had encouraged discrimination against Muslim women who wear headscarves, the report says.
As a result of the law, which was designed to uphold France’s tradition of separating state and religion, some women have been unable to marry, vote or take exams in a headscarf, it stated.
In the UK, the report says the media have created the impression that justice officials are successfully prosecuting Muslim terrorists, although only a few people have been convicted and the vast majority of those who are arrested on allegations of terrorism are released without charge.
In Germany meanwhile, more than 80% of those surveyed last year associated the world “Islam” with “terrorism” and “oppression of women” – although it was unclear to what extent this resulted in discriminatory behaviour.
It also says that Muslim schools in the Netherlands are widely believed to “undermine integration efforts” although it says such claims are “poorly supported by facts”.
A number of European countries have been engaged in a debate about whether long standing policies of multi-culturalism best serve the minorities involved.
Assimilation has been put forward as a means of stopping minorities – and particularly Muslims – from occupying a parallel society that could exclude them from mainstream benefits.
The IHF warns that “growing distrust and hostility” experienced by Muslims and a possible erosion of their confidence in the rule of law could also fuel support for extremist organisations.
The report makes a number of recommendations, including strengthening the law on racial discrimination and promoting systematic efforts to monitor discrimination.
It also advocates actively promoting tolerance among EU citizens by encouraging debate in the media over how to cover minorities and avoid “perpetuating prejudice”, and also recommends the setting up of elected Muslim representative bodies.
The IHF has a consultative status with the UN and the Council of Europe.