Ruth Kelly and other Catholic ministers will be expected to vote for Government plans to reform fertility laws, Labour sources said last night.
Under the Human Fertilisation and Embryology Bill ministers are proposing to remove the requirement on fertility clinics to consider the "need for a father" before providing IVF treatment.
The Bill also states that where a lesbian couple have engaged in a civil partnership, both will be entered as the legal parents.
The reforms have already been attacked by church leaders who consider it an attempt to undermine the traditional nuclear family.
Beginning its parliamentary passage in the House of Lords this week, the Bill was attacked by clergymen including Dr Sentamu, the Archbishop of York.
Cardinal Cormac Murphy-O'Connor, the leader of the Roman Catholic Church in England and Wales, said this week the Bill was "profoundly wrong", putting pressure on Catholics to oppose the reforms.
Ms Kelly, who has links to the conservative Opus Dei movement within the Catholic Church, has refused to say if she will support the Bill, despite orders to all Labour MPs to vote in favour of it.
Some Labour MPs have been angered by Government plans to enforce the party line, though the Bill touches on what many regard as "conscience issues".
Privately, Labour sources concede that the Bill will raise "serious problems" for Catholic MPs such as Ms Kelly and members with large Catholic populations in their constituencies.
But the growing unease among backbenchers has made it impossible for Labour whips and Alan Johnson, the Health Secretary, to grant exemptions for ministers such as Ms Kelly or to turn a blind eye if they choose to be absent on Government business.
One source said last night: "This is a Government Bill and it will be treated as such. That means a three-line whip will apply to all Labour MPs."
A spokesperson for Ms Kelly said last night that she had not even read the Bill yet. The spokesman said: "She has had no conversations with the whips' office about the Bill."
Ms Kelly's faith has frequently been at the centre of public controversy.
Last May, when she was the Cabinet minister responsible for equalities policy, she was criticised by gay rights groups for refusing to answer when asked if she believed homosexuality was a sin.
Earlier this year, Ms Kelly, 38, a mother of four, was said to be arguing within Government for Catholic abortion agencies to be exempt from equality laws forcing them to offer children to adoption by gay couples.
However, she may avoid a similar furore when asked to vote on new abortion laws.
Labour and Tory MPs are planning amendments that could lower the termination age from 24 to 20 weeks.
Labour MPs will be allowed a free vote on any abortion divisions.
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