The Pope has confirmed he will visit the UK later this year
The Pope has faced a backlash after urging Catholic bishops in England and Wales to fight the UK's Equality Bill with "missionary zeal".
Pope Benedict XVI said the bill - which could end the right of the Church to ban gay people from senior positions - "violates natural law".
But gay and human rights campaigners condemned his comments, and Labour MEP Stephen Hughes said he was "appalled".
Gordon Brown said he respected the Pope but commenting would be inappropriate.
The prime minister's official spokesman said Mr Brown had "enormous admiration and respect" for the pontiff, who will this year make the first papal visit to the UK since 1982.
The Pope told the Catholic bishops of England and Wales gathered in Rome: "Your country is well-known for its firm commitment to equality of opportunity for all members of society.
"Yet, as you have rightly pointed out, the effect of some of the legislation designed to achieve this goal has been to impose unjust limitations on the freedom of religious communities to act in accordance with their beliefs.
"In some respects it actually violates the natural law upon which the equality of all human beings is grounded and by which it is guaranteed."
Jonathan Finney, from gay rights group Stonewall, told BBC Radio 5 live: "People should not be denied access to services and employment purely because they are gay.
"We've got to guard against sweeping exemptions seeming to protect one person's freedom, which actually really impact on other people's."
He added: "What you can't start doing is saying that religious people have hard-won freedoms, we'll now restrict those, we won't give them to gay people, we won't give them to women."
Mr Hughes, speaking in Rome, said: "As a Catholic, I am appalled by the attitude of the Pope. Religious leaders should be trying to eradicate inequality, not perpetuate it."
He said the pontiff should ensure existing EU legislation was applied in the Vatican, rather than attacking equality in the UK.
The British Humanist Association said his "uninformed" and "homophobic" remarks came as no surprise and it would oppose his visit later in the year.
Head of public affairs, Naomi Phillips, said the Pope was seeking to discriminate against others in employment, services and education "unfettered by the laws that everyone else in society must abide by and respect".
But the head of the Catholic Church in England and Wales, Archbishop Vincent Nichols, said the Pope's words would resonate with many people who felt "uneasy" about the consequences of recent legislation.
He told BBC Radio 4's Today programme religious belief and practice had been driven into "the sphere of the private only", and the Pope wanted to express the "unjust limitations on the freedom of religious communities".
The Archbishop said: "He's [the Pope] not getting engaged in party politics... but he wants his reasoned voice - formed by the treasures of the Christian heritage which is deeply embedded in our culture - to be heard."
Religious leaders have voiced concern that the Equality Bill could force churches to employ sexually active gay people and transsexuals when hiring staff other than priests or ministers.
The National Secular Society said it would mount a protest campaign made up of gay groups, victims of clerical abuse, feminists, family planning organisations and groups supporting abortion choice, among others.
President Terry Sanderson said: "The taxpayer in this country is going to be faced with a bill of some £20m for the visit of the Pope - a visit in which he has already indicated he will attack equal rights and promote discrimination."
Human rights campaigner Peter Tatchell said the Pope's comments were a "coded attack on the legal rights granted to women and gay people".
"His ill-informed claim that our equality laws undermine religious freedom suggests that he supports the right of churches to discriminate in accordance with their religious ethos," he said.
"He seems to be defending discrimination by religious institutions and demanding that they should be above the law."
But Catholic MP Ann Widdecombe said: "This isn't a debate about homosexuality, this is a debate about religious freedom."
She told BBC Radio 5 live: "If a faith teaches, as major faiths do, that something is wrong, then quite clearly you cannot have somebody who believes that it's right actually occupying a very senior position.
"That we have accepted as natural justice for a very long time."
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Robert Mickens, Rome correspondent at the Catholic newspaper The Tablet, said the Pope's position was "nothing really new - this is part of the classic Catholic teaching on human sexuality".
"What the Pope is doing is trying to encourage the bishops to keep their resolve in very fluctuating morals in cultures and societies today."
Liberal Democrat MP Evan Harris, who sits on the Joint Committee on Human Rights, said all Britons - including Catholics and gay people - were protected by UK equality laws.
"Religious people can be reassured that there is nothing in the Equality Bill which imposes gay priests on religions, but it does protect the general workforce from prejudiced employers," he said.
A spokesman for the Government Equalities Office said: "The Pope acknowledges our country's firm commitment to equality for all members of society.
"We believe everyone should have a fair chance in life and not be discriminated against. The Equality Bill will make Britain a fairer and more equal place."