The Taoiseach, Mr Ahern, suggested in private exchanges with Cardinal Desmond Connell that the church leader misunderstood the issues surrounding the Government's support of controversial EU proposals to regulate embryonic stem-cell research.
Letters released under the Freedom of Information Act show that Mr Ahern wrote to the cardinal a month ago making a robust defence of the Government's decision to support regulations opposed by the church.
Mr Ahern also appeared to question the logic of the cardinal's position."I believe that failure to agree the guidelines could open the door to a significantly less restrictive regime for research funding. It is hard to see how creating such an opening can be compatible with the ethical concerns expressed regarding the principle of embryonic stem-cell research," he said.
"A decision not to oppose guidelines, equally, is not an expression of support for human embryonic stem-cell research."
EU industry ministers subsequently failed to agree regulations to govern the research. This means that EU funds for such work - in states where it is deemed permissible - will be drawn down once a moratorium on such work lapses at the end of the year. The funding cannot be used for Irish research because it is not deemed legal or ethical here.
While the Government holds out no hope of an agreement on regulations during the Irish presidency, it supported the regulations because it did not want unregulated research carried out elsewhere in the EU.
Records released under the Freedom of Information Act show that the Catholic bishops urged Mr Ahern on two occasions to change this position after he met a church delegation on October 29th.
Minutes from that meeting, which was publicised at the time, show that the church said it regarded the Government's likely support for the regulations as a matter of grave concern.
The Bishop of Clogher, Dr Joseph Duffy, wrote a week later to Mr Ahern saying it was "vital that the Irish Government should communicate . . . that it is indeed opposed to joint funding of research on human embryos and on embryonic stem-cells". He said the public impression was that the Government was neutral on the matter. "As we indicated at our meeting with you, we believe that this is an issue so fundamental that neutrality is not an option."
As the vote at the EU Council of Ministers approached, the cardinal wrote to Mr Ahern saying he was still hoping for a "good outcome".
He enclosed the text of a statement which contained a "personal appeal" to Mr Ahern and the Tánaiste, Ms Harney, to ensure that Ireland voted against the proposal "on the issue of allowing the EU to fund embryonic stem-cell research".
Mr Ahern sent a response to the cardinal on November 27th. "I greatly fear that your statement reflects a widespread misunderstanding of the issue which was before the council meeting," he said.
"The point being considered was not whether funds should be provided for stem-cell research: that is already part of the Sixth European Research Framework. What was for decision was whether there will be clear guidelines governing research funding for such projects."
Mr Ahern said the Government had taken great care when reaching its decision. "These guidelines secure our overriding concern, namely that funding is not provided for research which would be illegal or unethical in this country.
"I trust that you will see that our approach has developed carefully in recognition of that sensitivity and with a clear focus on the consequences of the outcome of the council's deliberations."
Dr Duffy also said in his letter that the bishops welcomed the Government's opposition to human cloning and euthanasia and welcomed the Government's support for a reference to Europe's Christian heritage in the EU constitution then under discussion.
He expressed appreciation of the opportunity for constructive exchange on issues of "fundamental significance" at the meeting of October 29th. "We welcome your proposal that we should continue to liaise with you," he said.
