Gay lecturers fear they will be at risk of greater prejudice as the church attempts to increase its influence over further education.
Most gay college staff believe religion is likely to come into conflict with their desire for equal treatment, according to a survey by the Centre for Excellence in Leadership.
The results came as church leaders continued their campaign for a greater presence in colleges, with Anglicans planning to double the number of chaplaincies, including representatives of all faiths.
Deborah Persaud, project leader for equality at the centre, said colleges such as Oldham had managed to combine active gay groups with a large, often conservative Muslim population - and claimed there was no evidence of any religion being damaging to gay lecturers.
The report nevertheless claims that homophobic bullying is rife in colleges and gets little attention: that staff and students are not told enough about equality for gay people; and that there is a lack of understanding about legal rights and responsibilities.
The Equality Act will ban discrimination against students on the grounds of sexual orientation, in addition to existing laws against discrimination or causing offence to gay employees.
Despite the perceived critical view of homosexuality in the Bible, a Church of England spokesman said: "There is no place for homophobia in the church.
People in intentionally permanent homosexual relationships are welcome in the church. Homosexual ordination is allowed in church.
"Homosexuals have the right not to be bullied. The church teaches that homosexuality is not God's ideal, and they should have the right to express that belief. Not all gay people think the same, not all Christians think the same. But we have freedom of speech and there has to be a balance."
The survey shows that gay male staff are more likely than lesbian colleagues to feel prejudice.
A third of gay men claim to have been passed over for promotion because of their sexual orientation. Nearly half of gay men and nearly a third of lesbians said their college was unfriendly to homosexual staff and students.
One gay principal said: "There are many principals for whom this is a no-go area. To be a junior staff member in a college with that sort of leadership will be difficult, especially for younger people who are used to being out.
I think it could still blight a career, unfortunately."
A university student union whose lesbian, gay and bisexual society displays posters in an FE college nearby said it will only allow people to visit in pairs due to a constant threat of violence.
A student, whose case was described as representative, said: "Every day, I walk through the college and people shout 'Faggot', 'Queer' or 'Shoot the faggot'.
"I try to ignore it now. I have complained to staff, to tutors and I went to see the principal. They just say, 'What can we do? Ignore it.'
"I can't ignore it really. If they called me a "black bastard", I might be able to get something done. They know that if they call me a 'Faggot', nothing will happen. I am scared, but I've got used to it."