Eighty per cent of the country's 1.8 million Muslims say they have been discriminated against because of their faith compared to 45% in 2000 and 35% in 1999, the Islamic Human Rights Commission (IHRC) said on Thursday.
Muslim men are now just as likely as women to experience prejudice - a significant change which the IHRC blamed on an increase in the number of police and security checks carried out on Muslim men since the September 11 attacks in 2001.
White British Muslims report more discrimination than any other ethnic group, suggesting Britons are intolerant of people who convert to Islam.
"What's happened, post 9/11, is that some very deeply rooted prejudices - things that weren't articulated in the public realm - have found expression," Arzu Merali, one of the authors of the report, said.
Eight per cent of the 1200 Muslims questioned in the survey said they experienced some sort of discrimination every day.
Another 8% said it was a weekly problem, 8% described it as monthly, and 55% said they had been discriminated against "on some occasions".
Only 15% said they had never experienced discrimination on the basis of their faith.
"The anti-terrorism laws are profiling and targeting Muslim men. Our case studies suggest nearly every Muslim man living in an urban area, particularly in London, has either been stopped and searched or knows someone who has"
Islamic Human Rights Commission
Eighty per cent of Muslim women complained of prejudice compared to 78% of men. In previous IHRC surveys the gender difference has been much more pronounced.
"The anti-terrorism laws are profiling and targeting Muslim men," Merali said. "Our case studies suggest nearly every Muslim man living in an urban area, particularly in London, has either been stopped and searched or knows someone who has."
In the past, she said, women were more readily identifiable as Muslims because of their dress and headscarves.
Now, however, Muslim men are equally visible - partly because the public has got used to seeing turbaned, bearded men on their television sets.
The IHRC, a research body and lobby group, urged the government to do more to promote positive images of Islam.
Muslims in the United Kingdom
suffered a backlash after 9/11
Britain's Muslims have long complained of an upsurge in abuse since the September 11 attacks and the subsequent war on terror, in which London has played a leading role.
Many Muslims feel they are viewed with suspicion by fellow Britons.
The government has vowed to bring in legislation to outlaw incitement to hatred on religious grounds. At present, such laws only exist to protect people on the basis of their colour, race, gender or ethnic origin.