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"I also hope that this announcement takes the focus away from a political row over a free vote and back onto the evidence on which politicians will need to consult their conscience."

Mr Brown said during a Labour local election launch in Hertfordshire: "I have always said that although I attach huge importance to this legislation – in saving lives and helping to cure and treat diseases – that we will respect the conscience of every Member of Parliament as they decide how to cast their vote in this," "On the three issues where, for the first time, these ethical issues are being debated in Parliament in this new way – and that’s so-called admix embryos, the second one is saviour siblings and the third one is IVF research – exercising your conscience will mean for Labour Party members a free vote.

"But the Bill itself cannot be subject to a free vote because there are so many other changes that I believe are necessary as part of building up the research framework of our country and, of course, creating the right ethical framework for the development of embryo research."

Mr Brown later announced that he would be writing to MPs to explain his position. "He will be setting out his reasoning as to why he supports those three clauses in a letter to Labour MPs later today," his spokesman said.

The Bill, which updates legislation first passed in 1990, will expand the scope of embryo research in several new areas. The Prime Minister says it is vital that it is passed to exploit progress towards treating and preventing conditions such as Parkinson’s, Alzheimer’s, cancer and heart disease.

The Catholic Church in Scotland cautiously welcomed Mr Brown's pledge of a free vote at the amendment stage, but said it was not enough. "This is a qualified free vote, it would only apply to amendments to the Bill, but the fact that Gordon Brown has belatedly acknowledged that there are conscience issues involved is better late than never," it said.

"The free vote aspect doesn’t change the fact that the Bill contains many deeply troubling proposals which could still be passed into law whether or not there is a free vote, so it’s important that MPs are well aware of the very controversial nature of these proposals."

Claire Curtis-Thomas, Labour MP for Crosby, indicated that she would defy the whips despite the new pledge.

"For some individuals, and that includes myself, this is a primarily moral question and at the end of the day I have to answer to my conscience and, at whatever stage this arises, I would not be able to agree with it," she told The World at One programme on BBC Radio 4.

Greg Hurst, Political Correspondent of The Times, said that today's developments had again left the Prime Minister open to charges of dithering, as it comes several days after the Conservatives and Liberal Democrats set out their position.

"Gordon Brown has clearly been forced into this rather messy compromise having whipped the Bill at every stage through the House of Lords," he said.

"The impact on the Bill is probably slight. Even if several dozen Labour MPs use the opportunity for free votes to oppose the three clauses identified, there are enough Conservative and Liberal Democrat MPs [who have already been promised a free vote] who are in favour to cancel them out.

"The damage to Gordon Brown is that he looks as though he has been indecisive in handling this issue, and has ended up being lectured by David Cameron in how to handle his own Labour MPs in the House of Commons.

"Mr Brown will now try to lead a campaign of persuasion to explain the purpose and benefits of this legislation ahead of the second reading in May."

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