The organs retention inquiry is concerned at the attitude of a number of hospitals which have failed to co-operate with its investigations to date.
The matter has been brought to the attention of the Minister for Health, Mr Martin, by the inquiry chairperson, Ms Anne Dunne SC.
In her progress report on the inquiry to the Minister, which has been seen by The Irish Times, Ms Dunne said there had also been a significant delay in the delivery of responses by certain other hospitals to the inquiry.
None of the hospitals are named. "At this stage, the inquiry does not think it appropriate to name any hospital," she wrote.
The inquiry, which began almost two years ago, is examining policies and procedures surrounding the removal, retention, storage and disposal of body parts without consent after post mortem examinations since the 1970s. It conducts its work in private.
Ms Dunne's report noted that while 150,000 pages of documentation had already been considered, progress was slow given the volume of work.
To date, it has received 402 submissions from parents and next of kin of those whose organs were retained, and oral submissions still have to be taken from 324 parents and next of kin.
"It is the opinion of the inquiry that the proper conduct of its work ...requires that it will be some considerable time before it is possible to present its (final) report to the Minister for Health and Children," Ms Dunne wrote.
The inquiry, which was established on a non-statutory basis and therefore is dependent upon the voluntary co-operation of all parties, covers all 201 hospitals in the State.
Some 62 of these have signed documentation to say they accept the procedures being followed by the inquiry. Among the 62 are six of 11 hospitals named in the inquiry's terms of reference.
"The inquiry has, in relation to a small number of hospitals in this category, concerns of varying degree, as to the attitude of these hospitals to the inquiry," the report said.
"A number of hospitals have raised legal issues in relation to their co-operation with the inquiry, and have sought to rely on the Abbeylara decision to postpone or delay any such co-operation. The inquiry awaits the Attorney General's advice in this matter through the Department of Health and Children."
Nonetheless, Ms Dunne went on to point out that no hospital notified the inquiry of "its definite unwillingness to co-operate".
The response of many other parties, including pharmaceutical companies, on the issue of procurement and use of pituitary glands in human growth hormone treatment had been helpful, the report added.
To date, Ms Dunne's work has included reviewing submissions, attending a Dublin hospital to see a post mortem at first hand, and travelling to the US to acquaint herself with post mortem policy.
The Parents for Justice Group, which had campaigned for the inquiry, recently called for the inquiry to be stood down and withdrew its co-operation. It had complained, among other things, that Ms Dunne's progress report was not published, and had to be sought by them under the Freedom of Information Act.