Muslims, pagans and members of Christian sects such as Mormons or Jehovah’s Witnesses are most likely to experience "substantial" unfair treatment because of their beliefs – especially at work and in the criminal justice system.
Researchers from the Universities of Derby, Manchester and Oxford said it was lesser-known "new" religions, which might include branches of Christianity or movements like Scientology or the Unification Church known as Moonies, where people experienced the greatest discrimination.
Paul Weller, Professor of Inter-Religious Relations at the University of Derby, who led the study, told The Huffington Post UK: "We noticed a particular frequency and severity in the complaints relating to these religions.
Pagans sometimes conceal their religion for fear of discrimination
"There are many instances of discrimination against Christians, but the discrimination against new religions is more "in-your-face", verging on hatred.
"For Pagans, many of them have kept their religion secret, for fear it would be misunderstood."
But it also found new examples of unfair treatment of Christians, with many telling researchers issues they had with being made to work on a Sunday.
"Non-religious" people interviewed in the study said they believed Christians received privileged treatment, especially in education and in governance, like having bishops in the House of Lords or prayers at council meetings.
The research was looking into how new religious discrimination law had affected people reporting religious discrimination.
Professor Weller said: "A decade ago it was not illegal in England and Wales to discriminate on grounds of religion or belief, so at that time those who reported unfair treatment on the basis of religion or belief had little scope for remedy.
"Because we are seeing more reporting of the discrimination, our interim findings show that people seem to have been empowered by the legislation.
"But many know the protection exists, but aren’t sure how to pursue redress after they feel it has happened to them."
The researchers are now planning a series of workshops across the country, asking for feedback from religious and non-religious people, lawyers, businesses and community groups
The interim findings were based on interviews with over 230 participants from religious groups in five different areas, a survey of 500 people, focus groups with 40 non-religious and a review of over 130 legal cases.