The Taoiseach, Mr Ahern, has said that there are doubts over whether Irish law prohibits embryonic stem-cell research in the State.
It emerged yesterday that Mr Ahern told the Fianna Fáil parliamentary party last Tuesday there may be no protection in Irish law against such research being carried out.
This contradicts the common view that the constitutional protection of the life of the unborn would prohibit such work taking place here.
This is significant because there is no statutory prohibition on this research.
The chairman of the Fianna Fáil parliamentary party, Mr Seamus Kirk, confirmed that last Tuesday Mr Ahern expressed doubt about the legal status of work undertaken outside the framework of the EU research programme. Mr Kirk said there was "some uncertainty as to what the legal position is" but did not elaborate on this.
Informed sources said the uncertainty concerned privately funded research.
By contrast, the European Commission guidelines, now the subject of controversy, will govern only research funded by the EU.
Sources said these regulations went beyond Irish law because they state that EU-funded research can be carried out only in states where it is legal and deemed ethical.
The sources said protection against embryonic stem-cell research in this State came from the guidelines of the Irish Medical Council, which hold that such work is unethical.
While the council's guidelines prevent Irish doctors giving frozen embryos to scientists for privately funded stem-cell research, the sources said it might be open to those researchers to source frozen embryos or stem lines abroad.
This view was endorsed last night by the Green MEP, Ms Nuala Ahern. She said: "I think it is very possible that you could find a situation where private research was carried out in this country without the ethical guidelines that we are supposed to be pursuing in Europe."
The former taoiseach, Mr John Bruton, said the Government should not support a Portuguese proposal for a more restrictive EU framework for stem-cell research on embryos.The Fine Gael TD said the amendment proposed by Portugal was not a compromise, but a slightly nuanced acceptance of the European Commission's original proposal.
"The Tánaiste should take a clear position on this issue and should stop using procedural smokescreens to evade a very simple ethical decision," Mr Bruton said.
The compromise, which is backed by the Government, still involved "acceptance of the principle that it is alright to use Irish taxpayers' money to pay for research involving the killing off of potential human lives", he said.
Portugal tabled the proposal at the meeting in Brussels of the European Council of industry ministers. The amendment would narrow the scope of the original European Commission framework by confining research to stem-lines already drawn from embryos and in storage before November 26th.
