The government is right to try to push through controversial embryo laws, Health Minister Ben Bradshaw has said.
The Archbishop said many MPs are troubled by the bill
Legislation would be "to the potential benefit of many people in this country", Mr Bradshaw told the BBC.
But the Archbishop of Cardiff, the Most Reverend Peter Smith, said he advised MPs to vote against parts of the bill.
He said MPs have a "moral dilemma" over the bill and has written to the prime minister asking for them to be allowed to vote in line with their conscience.
The Human Fertilisation and Embryology Bill would allow the creation of hybrid human-animal embryos for research.
'Sacredness of life'
The archbishop told BBC Radio 4: "Those MPs who have approached me over recent weeks have said: 'Look, I don't think this is right. I accept the teachings of the Church, yet I am a Government minister, or I am a Labour MP. Can I discuss with you the moral dilemma I have got?'.
"This is a matter which is clearly affecting many MPs.
"I have written to the Prime Minister myself asking him that, in view of these very important issues which touch on the sacredness of human life, its meaning and purpose, would he please grant a free vote, because that is what is really required."
Welsh Secretary Paul Murphy is reportedly one of those prepared to quit the Cabinet rather over the bill. Other Catholics in the Cabinet are Transport Secretary Ruth Kelly and Defence Secretary Des Browne.
The bill has also been condemned by other leading Catholics.
Catholic Labour MP Joe Benton and Scottish Catholic leader Cardinal Keith O'Brien are among those who have called for MPs to have a free vote.
In a sermon to be delivered on Easter Sunday, Cardinal Keith O'Brien described the plans as "monstrous".
He warned Mr Brown against imposing a three-line whip on Labour MPs - which orders them to vote with the party line.
Another Catholic MP, Stephen Pound, has said he will not be voting for the measure.
He said: "We seem to be moving into a sphere where we are actually taking on the role of the creation of life."
Responding to Cardinal O'Brien's criticism, Mr Bradshaw told BBC Radio 4's Any Questions: "If it was about the things the cardinal referred to, creating babies for spare parts or raiding dead people's tissue, then there would be justification for a free vote.
"But it's not about those things. He was wrong in fact, and I think rather intemperate and emotive in the way that he criticised this legislation.
"This is about using pre-embryonic cells to do research that has the potential to ease the suffering of millions of people in this country. The government has taken a view that this is a good thing."
Liberal Democrat Evan Harris, a member of the Commons Innovation, Universities, Science and Skills Select Committee, said he felt ethically obliged to allow scientists to carry out the research.
"From a religious point of view, it seems right that we should use God-given powers of science to create short-term entities that are microscopic that might be a way of showing us how to develop stem cells from embryos that might be used to treat people with terrible diseases," he said.
Downing Street said a decision on a free vote would be taken "in due course".
Both the Conservative and Liberal Democrat leaders plan to allow their MPs to have a free vote on the more controversial aspects of the bill.
The Human Fertilisation and Embryology Bill is designed to bring the 1990 regulatory framework for fertility treatment and embryo research in line with scientific advances.