Gordon Brown is to give Labour MPs permission to oppose parts of the controversial Human Fertilisation and Embryology Bill, according to reports.

The BBC said on Sunday that the prime minister is to allow backbenchers to defy the whip as long as they do not prevent the passage of the legislation through Parliament.

Catholic MPs and ministers are understood to be particularly keen to avoid supporting sections of the Bill on allowing scientists to create embryos which combine human DNA and animal cells, which the government argues is crucial to advancing scientific research.

Health secretary Alan Johnson told BBC News 24: "For people out there suffering from Parkinson's disease and motor neurone disease, this is not a question of some issue about the procedure through the House of Commons.

"This is an issue about whether we can find the drugs that can cure their illnesses. So this is the heart of the matter."

Brown has been under pressure to grant a free vote, as the Conservative and Liberal Democrat leaders have said they will, with the former Labour minister Stephen Byers saying on Sunday the public would "look on in disbelief" if he did not.

However he is now seeking a compromise that would allow opposition to some amendments, but not the Bill as a whole.

Northern Ireland secretary Shaun Woodward suggested a compromise was possible.

"I believe it is possible, if we listen to the arguments and we remove the misunderstandings, to find a way forward so the government can complete its business," he told Sky News.

The indication followed fresh calls from the head of the Catholic church in England and Wales on the issue.

In an interview for Sky News on Sunday Cardinal Murphy-O'Connor said: "I think Catholics in politics have got to act according to their Catholic convictions, so have other Christians, so have other politicians.

"There are Catholics who feel very strongly about this matter and I am glad that they do.

"Certainly, there are some aspects of this Bill on which I believe there ought to be a free vote, because Catholics and others will want to vote according to their conscience. I don't think it should be subject to the party whip."

Brown is also set to allow some Catholic ministers to abstain on key votes.

Wales secretary Paul Murphy is thought to be prepared to resign rather than support the Bill.

And the Archbishop of Cardiff the Most Reverend Peter Smith told BBC Radio 4 he had discussed the concerns of some members of the government.

"Those MPs who have approached me over recent weeks have said: 'Look, I don't think this is right. I accept the teachings of the Church, yet I am a government minister, or I am a Labour MP. Can I discuss with you the moral dilemma I have got?'," he said.

"This is a matter which is clearly affecting many MPs.

"I have written to the prime minister myself asking him that, in view of these very important issues which touch on the sacredness of human life, its meaning and purpose, would he please grant a free vote, because that is what is really required."

Meanwhile on Monday fertility expert Lord Winston criticised statements made by the head of the Catholic church in Scotland.

In his Easter sermon Cardinal Keith O'Brien described the legislation as a "monstrous attack on human rights, human dignity and human life" which would allow experiments of a "Frankenstein proportion".

However the Labour peer told the Daily Telegraph: "They are misleading and I'm afraid that when the Church, for good motives, tells untruths, it brings discredit upon itself."