The minister for health at the time the Madonna House report was completed wanted to publish it in full, but received legal advice against doing so.
"My instructions to officials was to publish the lot," Mr Michael Noonan told The Irish Times. "Then the advice came back that we could not, and I said to publish what we can.
"It was discussed in Cabinet and at programme manager and party leader level," he said. "We wanted to get it published."
Mr Brendan Howlin, the minister for health when the issue of Madonna House first arose, said: "The Government was frenzied about it." He pointed out that the issue which brought down the government in 1994 was the delay in dealing with the Brendan Smyth extradition. "We were very sensitive to it."
The decision on publishing the report was not made in cabinet, and there was no memorandum to cabinet on it, he said. Mr Howlin was a member of the two governments in office while the report was being compiled.
There was no such formal decision because the report was not a departmental one, but had been commissioned by the order which ran the home, the Irish Sisters of Charity, according to Mr Noonan.
There were three legal considerations in the decision not to publish the full report, according to a briefing document seen by The Irish Times.
These were that prosecutions pending or in prospect should not be compromised; that the identity of the victims should not be revealed; and that there was "a serious risk of committing grave contempt and defamation" in substantial parts of the report.
The deletions from the report were made on the recommendation of counsel retained by the Chief State Solicitor, and not by the Department of Health or either of the parties involved, that is, Madonna House or the Eastern Health Board, according to the document.
The report was commissioned by the order which ran Madonna House, the Irish Sisters of Charity, and chaired by Mr Fred O'Donohue, a former senior executive of the Eastern Health Board, which financed it. Mr O'Donohue had been the programme manager for community care at the time, and had just retired when asked to chair this inquiry. He has since died.
The inquiry followed a report on the Kilkenny incest case, which was published in full. That inquiry had been set up by the minister for health, Mr Brendan Howlin, under the chairmanship of Ms Justice McGuinness. There was no independent report on the running of Madonna House.
According to the departmental briefing document, while the Department did not commission the report, "the then Minister Brendan Howlin was determined that an inquiry would take place and, in that sense, the Department was very much involved in the decision to go ahead with the inquiry in the format in which it proceeded."
A file on the abuse in Madonna House did go to the Director of Public Prosecutions, and this was one factor in the decision not to publish the entire report. However, the DPP then decided not to prosecute.
This decision allowed certain sections to be published, according to Mr Noonan, but the issues of identifying the victims and defaming certain individuals still remained. "Any comment about the management would have identified one individual," he told The Irish Times.
Asked if the report could not have been written in a way which would not have risked identifying the children, or defaming any individual, he said: "You are right. All the facts could have been brought out."
He added that States of Fear was a very good programme.