The Taoiseach, Mr Ahern, and the Tánaiste have strongly rejected a claim by a Fianna Fáil backbencher that Ms Harney failed to inform the Cabinet about an EU decision two years ago to sanction stem-cell research on embryos.
A Government spokesman last night accused the Cork TD, Mr Batt O'Keeffe, of making "mischievous and false" claims about Ms Harney's role in the EU decision in December 2001.
The Tánaiste will vote today in Brussels in favour of an EU framework to govern the research sanctioned by that decision.
While the Cabinet endorsed her stance yesterday, Mr Ahern came under sustained pressure at a Fianna Fáil Parliamentary Party meeting over the Government's support for the framework.
The chairman of the parliamentary party, Mr Séamus Kirk, said Mr Ahern had mollified concerns within the party. "I think there's a clearer understanding of what's involved."
But not a single member spoke in favour of the Government decision.
"Just about everybody who spoke opposed or expressed reservations about the the whole issue of stem-cell research on embryos," said one TD last night.
Mr O'Keeffe's intervention came after the meeting, when he said Mr Ahern and the Minister for Health, Mr Martin, had made it "quite clear" to the meeting that Ms Harney played a central role in the decision to fund stem-cell research on embryos without Cabinet approval.
On RTÉ television, he said: "During the course of the debate, the Minister for Health and the Taoiseach responded ... that the decision to fund embryo stem-cell research and other research was taken 18 months ago.
"There was no Cabinet decision, this was a question I asked myself. It was a decision, we were told at the meeting, taken by the Tánaiste 18 months ago to be part and parcel of the funding of embryo research and other research, stem-cell research, in Europe and that €1.1 billion was put in place at that time."
The Government responded immediately with a statement endorsed by Mr Ahern and Ms Harney.
It said: "Any claim that the Tánaiste, Mary Harney, took a unilateral stance on the issue of stem-cell research is mischievous and false." It said the then minister of state, Mr Noel Treacy, had "first" agreed to support the research programme and its funding.
Mr O'Keeffe rejected this last point, saying ultimate responsibility rested with the Tánaiste.