Gordon Brown is “following the precedent set in 1990 with the original Human Fertilisation and Embryology Bill” in allowing his MPs a free vote on measures that ensure gay equality and allow for the creation of animal-human embryos for research purposes.

Roman Catholic Labour MPs are expected to challenge the removal of a requirement for doctors to “consider the need for a father” when deciding to consent to IVF or assisted conception treatments.

The bill proposed to replace that with a need for “supportive parenting.”

Many lesbians are refused treatment by doctors under the present arrangements.

A Downing St spokesman said the Prime Minister personally supports that change to the law.

He has written to all Labour MPs explaining his position.

While the government’s position remains that given the legal recognition of civil partnerships and laws preventing discrimination on the grounds of sex and sexual orientation, retaining any provision that mentioned a mother and a father is inconsistent with the wider government policy of promoting equality.

The Prime Minister’s spokesman called the bill “an important piece of Government business; it was in the Queen’s Speech and it was the Prime Minister’s view that it was important that the bill as a whole was passed.”

He pointed out that all Labour MPs would be expected to support the bill as a whole in its later stages.

“We had always said that this would be treated as government business but we would find a mechanism by which individual MP’s could express their conscience and that was what we were doing,” he said.

He confirmed that Mr Brown had been in contact with Cabinet colleagues and others on the issue.

As many as 12 ministers, three of them in the Cabinet, were reported to be considering leaving the government rather than vote for parts of the bill.

The Prime Minister’s spokesman said that “it was worth bearing in mind we were still several months away from the actual vote-taking place on the bill.

“So in terms of the whipping arrangements being set out today, it was much earlier than would normally be the case.”

Labour MPs will be allowed a free vote on two other clauses in the Human Fertilisation and Embryology Bill, which allow the creation of human-animal embryos for medical research and the creation of so-called “savour siblings,” who would aid a sick brother or sister.

For more information on saviour siblings click here.

For more information on human-animal embryos click here.