The Pontiff said the effects of some legislation designed to give equality of opportunity had been to impose "unjust limitations" on the freedom of religious communities to act "in accordance with their beliefs".
"Your country is well-known for its firm commitment to equality of opportunity for all members of society," he told the Catholic bishops of England and Wales gathered in Rome.
"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."
His remarks have been interpreted as an attack on the Sexual Orientation Regulations which forced Catholic adoption agencies to consider gay couples as potential adoptive parents.
By the time the regulations came into force in January last year, five of the agencies in England and Wales had cut ties with their Roman Catholic dioceses in order to comply with the new laws.
The Government also suffered defeats in the House of Lords last week after the churches voiced concerns that the provisions of the flagship Equality Bill could expose them to legal challenges if they refused to employ sexually active gay people and transsexuals.
The Pope's remarks were made in an address in which he gave the first official confirmation that he will make his first apostolic visit to Britain later this year.
No dates or itinerary were given, but the Pope, who will be 83 when he visits, spoke of the "living faith and devotion" among Catholics in England and Wales, highlighting the recent visit of the relics of St Therese and the forthcoming beatification of Cardinal John Henry Newman.
"On the occasion of my forthcoming apostolic visit to Great Britain, I shall be able to witness that faith for myself and, as successor of Peter, to strengthen and confirm it," he told the bishops.
"During the months of preparation that lie ahead, be sure to encourage the Catholics of England and Wales in their devotion, and assure them that the Pope constantly remembers them in his prayers and holds them in his heart."
The Pope is widely expected to visit England and Scotland in a four-day trip between September 16 and September 19.
The visit is expected to have many of the trappings of a state visit, according to reports.
The beatification of Cardinal Newman, bringing him a step closer to becoming England's first non-martyred saint since the Reformation, will possibly be held in a ceremony at Coventry Airport, it has been reported.
The last Papal visit to Britain was in 1982, when Pope John Paul II visited England, Wales and Scotland.
The National Secular Society (NSS) said it would mount a protest campaign against the visit made up of gay groups, victims of clerical abuse, feminists, family planning organisations and pro-abortion groups among others.
NSS president Terry Sanderson said: "The taxpayer in this country is going to be faced with a bill of some £20 million for the visit of the Pope.
"A visit in which, he has already indicated, he will attack equal rights and promote discrimination.
"We have a petition online where people can make clear their opposition to the state funding of this visit."
Human rights campaigner Peter Tatchell said: "The Pope's criticism that British equality legislation 'violates the natural law' is 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 seems to be defending discrimination by religious institutions and demanding that they should be above the law."
A spokeswoman 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."
Dr Evan Harris, Liberal Democrat equality spokesman, said: "Britain's equality laws protect both Catholics and gay people from unfair discrimination, and in employment we are governed by exactly the same rules as Catholic Italy.
"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."
Archbishop Vincent Nichols, head of the Catholic Church in England and Wales, told the BBC Radio 4 Today programme: "I think (the Pope's) words will find an echo in many in our country who are uneasy that perhaps one of the unintended consequences of recent legislation is to drive religious belief and practice into the sphere of the private only."
He went on: "The way in which our public life is organised is something to which everybody has a right to contribute. He is certainly not getting involved in party politics... but he wants his reasoned voice - formed by the treasures of the Christian heritage which is deeply embedded in our culture - he wants that voice to be heard.
"It is a reasoned voice, and I think he has every right to express the concerns of many."
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