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.
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.
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."
The Express