Health Minister Dr James Reilly has said that the one outstanding issue of clinical guidelines "are a matter for clinicians and totally out of our control".
And he said the clinical guidelines for obstetricians would be coming from the Institute of Obstetricians and Gynaecologists (IOG).
But IOG chairman Professor Robert Harrison said he wanted to set the record straight. He pointed out that the guidelines were being devised by a working group set up by Dr Reilly's own department.
"The guidelines are coming from the Department of Health, not directly from the Institution of Obstetricians and Gynaecologists," he said.
It is understood that the working group's clinical guidelines for doctors on how to implement the abortion law have been delayed by the range of different medical professionals involved. It has to take account of the views of obstetricians, GPs and psychiatrists.
The 12-member group contains ten representatives of the medical professions, one representative from the Department of Health and one from the HSE Corporate section. It is chaired independently by Dr Declan Bedford, a specialist in public health medicine.
The group met for the first time on September 24 last year.
Prof Harrison said that his institute saw the need to make sure that the clinical guidelines for the abortion legislation were drawn up correctly.
"I don't think there's any controversy at all. This is a very tricky thing. I think they are wise to take their time and get it right," he said.
In a recent interview, Dr Reilly has said that the guidelines will be in place "very early in the New Year". But he said that abortions can be carried out without them.
"You can. Absolutely. Totally. The most important thing you need is the panel of experts to review an appeal case," he said.
Under the legislation, a panel of doctors will have to give the go-ahead for an abortion where they believe there is a real and substantial risk to the life of a mother, including threat of suicide.
Doctors have been signed up to these panels, as well as the appeal panels for women who believe they have been wrongly refused permission for an abortion. A spokesman for Dr Reilly said the working group was set up to prepare high-level inter-professional guidance to implement the Protection of Life During Pregnancy Act
The abortion law was hugely controversial, with five Fine Gael TDs and two Fine Gael Senators losing the party whip for refusing to vote in favour of it.
Around 25 hospitals in the State will be authorised to carry out abortions in these circumstances under the provisions of the Act.