Labour MPs will not be given a free vote on the Human Fertilisation and Embryology Bill it has emerged.

Traditionally members are given a free vote on issues deemed to be a matter of conscience.

However, growing backbench unease about the proposals has led government sources to confirm that the bill will be subject to a three-line whip, meaning all Labour MPs must vote in favour of it.

The Lords will continue their debate in the second reading of the bill today.

Roman Catholic MPs such as cabinet minister Ruth Kelly could face a dilemma if asked to defy the church and vote in favour of the bill.

The legislation regulates animal/human embryo hybrids, allows new cloning techniques to eliminate life-threatening inherited illnesses and updates rules around the use of embryos.

The Bill includes recognition of same-sex couples as legal parents of children conceived through the use of donated sperm, eggs or embryos.

For example, a woman who gives birth and her civil partner will both be recognised as the parents of a child conceived by assisted reproduction.

Two men will be able to apply for a parental order to become parents of a child conceived through a surrogacy arrangement.

The leader of Britain’s Catholic Church, Cardinal Murphy-O’Connor, criticised the bill, saying that it is “profoundly wrong.”

In a letter to The Times, he claims that it subordinates the rights of the child to the desire of the women.

“The bill proposes to remove the need for IVF providers to take into account the child’s need for a father when considering an IVF application, and to confer legal parenthood on people who have no biological relationship to a child born as a result of IVF.

“This radically undermines the place of the father in a child’s life, and makes the natural rights of the child subordinate to the desires of the couple. It is profoundly wrong.”

Ms Kelly’s religious beliefs caused controversy in her previous role in government.

As Communities Secretary she delayed the Sexual Orientation Regulations, rules to outlaw discrimination on the grounds of sexual orientation in the provision of goods and services.

They came into force in April, four months later than previously envisaged.

The thousands of responses that the Department for Communities and Local Government received during the consultation process was the reason given for the delay.

Many gay rights activists feared that Kelly was attempting to stall the regulations so that she could amend them to reflect the concerns of religious groups.

She was involved in further controversy over a proposed opt-out for Roman Catholic-run adoption agencies from the regulations.

Amendments to the Human Fertilisation and Embryology Bill that seek to lower the legal limit at which a woman can seek an abortion will be subject to a free vote.