With its constituency of five million members - including a number of senior Cabinet ministers - the Church has proved a serious irritant to Gordon Brown.
Senior Catholic leaders, traditionally aligned with Labour, have unequivocally - and very publicly - voiced opposition to Labour MPs being told to support the legislation, forcing ministers to consider a compromise solution.
The Archbishop of Westminster, Cardinal Cormac Murphy-O'Connor, has called for a free vote "because Catholics and others will want to vote according to their consciences", while Scotland's Cardinal Keith O'Brien has described plans to allow the creation of part-human, part-animal embryos as "monstrous".
"It is difficult to imagine a single piece of legislation which more comprehensively attacks the sanctity and dignity of human life than this particular Bill," he said.
"The Government has no mandate for these changes: they were not in any election manifesto, nor do they enjoy widespread public support. One might say that we are about to have a public Government endorsement of experiments of Frankenstein proportion - without many people really being aware of what is going on."
The outspoken comments have attracted considerably more attention than the Conservative Party's criticisms of Mr Brown over the issue, and may yet provide the pressure necessary for the Prime Minister to back down and allow Labour MPs to vote as they wish.
That pressure has been intensified by three Catholic Cabinet ministers - Ruth Kelly, the Transport Secretary, Des Browne, the Defence Secretary, and Paul Murphy, the Welsh Secretary - who are said to be resisting parts of the Bill that conflict with their beliefs.
In recent years, Catholic-based pressure groups have grown in stature and express increasingly strong views about issues that run counter to their doctrine.
Catholic Action UK, which was set up in the summer of 2006 to "facilitate protests by faithful Catholics against attacks on the Church and morality in the United Kingdom", has helped quash the Government's attempts to admit 25 per cent non-Catholic pupils into Catholic schools and a euthanasia Bill.
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