"The thing I've become anxious about in recent times is this – there is certainly a feeling amongst some people of belief that they are under siege, that they are often disadvantaged, that they are looked at and considered in some way different and their faith makes them less worthy of regard," he said.

"There is a view that says religion is a private matter and it's entirely a choice. I think that's entirely not right. "Faith identity is part of what makes life richer and more meaningful for the individual. It is a fundamental part of what makes some societies better than others in my view.

"I understand why a lot of people in faith groups feel a bit under siege. They're in a world where there are a lot of very clever people who have a lot of access to the airwaves and write endlessly in the newspapers knocking religion and mocking God. The people who want to drive religion underground are much more active, much more vocal.

There is no doubt there's quite a lot of intolerance towards people of faith and towards belief.

"There's a great deal of polemic which is anti-religious, which is quite fashionable. People can sometimes think we're part of that fashionable mocking and knocking brigade. We're not that."

Standing up for believers

The equality watchdog chairman said it would support believers who suffer discrimination because of their faith, and conceded there was a perception it had not done so in the past.

"That is slap bang in the middle of our anti-discriminatory work," he said.

"Being an Anglican, being a Muslim or being a Methodist or being a Jew is just as much part of your identity and you should not be penalised or treated in a discriminatory way because of that. That's part of the settlement of a liberal democracy.

"Our business is defending the believer. The law we're here to implement recognises that religious identity is an essential part of this society. It's an essential element of being a fulfilled human being.

"My real worry is that there are people who may well feel they're being treated unfairly because of their faith and who actually in fact may be being treated unfairly because of their faith but for some reason feel they can't get our support in getting justice."

Warning to churches on charity

The quid pro quo for standing up for individual believers is that churches and faith groups have to fall into line with the views of wider society to keep their charitable status, Mr Phillips signalled.

"Churches, mosques, temples, religious organisations of all kinds now have to some extent protection under the law but they also have to obey the law including anti-discrimination law because they are charities, because they offer a public service," he said.

"People are being confused about the right of the individual to freedom of conscience and freedom of expression and the freedoms of particular institutions or organisations.

"Nobody is going to say that its OK for a Muslim community to apply in isolation and override the view of the civil courts that says a woman's testimony is worth less than a man's."

Mr Phillips says that the refusal to allow Catholic adoption agencies an exemption from laws stating homosexual couples could not be discriminated against was even more clear cut.

"Catholic care was a clearer and simpler case. You're offering a public service and you're a charity and there are rules about how charities behave. You have to play by the rules. We can't have a set of rules that apply to one group of people simply because they happen to think it's right."

No politics beyond church door

Equality laws should not impinge on the way that religious institutions are run, Mr Phillips said - meaning gay bishops and women priests are not a matter for his watchdog.

"It's perfectly fair that you can't be a Roman Catholic priest unless you're a man," he said.

"It seems right that the reach of anti-discriminatory law should stop at the door of the church or mosque.

"At the moment the law says it [appointing openly gay bishops] is a matter for the Church of England. It's probably right.

"I'm not keen on the idea of a church run by the state. I don't think the law should run to telling churches how they should conduct their own affairs."

Political Christians

A string of high-profile legal cases involving Christians who feel discriminated against because of objections to homosexuality may be fuelled by evangelical activists who are seeking political influence - not helping their religion - he warned.

"I think the most likely victim of actual religious discrimination in British society is a Muslim but the person who is most likely to feel slighted because of their religion is an evangelical Christian," he said.

"There are a lot of Christian activist voices who appear bent on stressing the kind of persecution that I don't think really exists in this country. There are some Christian organisations who basically want to have a fight and therefore they're constantly defining the ground in such a way that anyone who doesn't agree wholly agree with them about everything is essentially a messenger from Satan.

"I think for a lot of Christian activists, they want to have a fight and they choose sexual orientation...