Churches and faith groups must fall into line with the views of wider society to keep their charitable status, according to the chairman of the UK’s Equality and Human Rights Commission Mr Trevor Philips.

He accused Christians of being more militant than Muslims when it came to complaining about discrimination.

However, he conceded that there is “a lot of anti-religious noise” in Britain today.

In an interview with the Sunday Telegraph, ahead of a wide-ranging report on religious discrimination, Mr Philips said that Churches and religious institutions had to comply with equality legislation when they delivered services to the public as a whole.

And he added that he thought some Christian groups were picking fights for their own political ends.

“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.”

However, he admitted that his body had not been seen to stand up for the people discriminated against because of their faith in the past.

And he expressed concern that people of faith were “under siege” from atheists whom he accused of attempting to “drive religion underground”.

Mr Phillips spoke after a series of high-profile cases which have featured Christians claiming they have been discriminated against because of their beliefs, with a doctor currently fighting a reprimand from the General Medical Council for sharing his faith with a patient.

While the equalities boss promised to fight for the rights of Christians, he expressed concern that many cases were driven by ‘fundamentalist’ Christians who are holding increasing sway over the mainstream churches because of the influence of African and Caribbean immigrants with “intolerant” views.

In contrast, he said Muslims were less vociferous because they are trying to integrate into British “liberal democracy”, he said.

“Muslim communities in this country are doing their damnedest to try to come to terms with their neighbours to try to integrate and they’re doing their best to try to develop an idea of Islam that is compatible with living in a modern liberal democracy.

Senior Church of England clerics, including Lord Carey, the former Archbishop of Canterbury, have attacked equality laws for eroding Christianity and stifling free speech.

But Mr Phillips said: “I think the whole argument isn’t about the rights of Christians. It’s about politics. It’s about a group of people who really want to have weight and influence.”

However, Mr Phillips said he understood why a lot of people in faith groups “feel a bit under siege,” he said.

“There’s no question that there is more anti-religion noise in Britain.

“There’s a great deal of polemic which is anti-religious, which is quite fashionable.”

Phillips said that the Commission is committed to protecting people of faith against discrimination and also defended the right of religious institutions to be free from Government interference.

The Church of England is under pressure to allow openly gay clergy to be made bishops, while the Catholic Church only permits men to be priests, but the head of the Government-funded equalities watchdog said they are entitled to rule on their own affairs.

“The law doesn’t dictate their organisation internally, in the way they appoint their ministers and bishops for example,” he said.

“It’s perfectly fair that you can’t be a Roman Catholic priest unless you’re a man. It seems right that the reach of anti-discriminatory law should stop at the door of the church or mosque.”