No Catholic bishop in the State complied fully with a request by the HSE to supply all information received by his diocese on allegations of clerical child sex abuse.
A spokeswoman for the Office of the Minister for Children, which has received the findings of a national audit of child protection practices, said the bishops "felt unable" to supply all the requested information, as this presented "insurmountable difficulties".
The HSE request for such information, in October 2006, was made as it began preparing the national audit of the child protection practices of Catholic dioceses in the Republic, which is to be presented to the Cabinet on Wednesday.
Absent from the audit are such allegations as the one that prompted the inquiry which led to child protection practices in Cloyne diocese being described, in a report on December 19th last, as "inadequate and in some respects dangerous".
That conclusion was drawn by the Catholic Church's own independent watchdog, the National Board for Safeguarding Children (NBSC), following an investigation into child protection in Cloyne last spring.
The investigation followed allegations which came through the One in Four group and the Faoiseamh helpline for abuse victims.
These allegations were not included in information supplied to the HSE by Cloyne during the audit process.
A spokeswoman for the Office of the Minister for Children confirmed that the Catholic bishops "felt unable" to complete the HSE questionnaire sent out as part of its national audit.
She said "the formal audit commenced with the issue of a questionnaire to the Bishops and Religious Conference (the religious congregations) on 23rd of October, 2006".
She added:"On receipt of the questionnaire the bishops, using identical concerns, advised that, whilst anxious to co-operate fully with the HSE, in the absence of the legislative measures anticipated by the Ferns Report, they were unable to do so in respect of Section 5 of the planned audit.''
She explained that "this Section 5 sought detailed information on complaints and allegations of child sexual abuse against members of the clergy, and whether these allegations had or had not been brought to the attention of civil authorities".
"The bishops identified that Section 5 presented insurmountable difficulties in relation to confidentiality, given that appropriate legal arrangements had not been put in place,'' said the spokeswoman for the office.
She said: "The HSE obtained legal advice and on this basis decided to proceed with the audit with the exception of Section 5."
It is believed that the bishops were concerned about defamation issues and the constitutional right of an individual to a good name, as well as being in breach of confidence when it came to passing on so-called "soft" information suggesting abuse.
The spokeswoman said that a joint Oireachtas committee had recommended legislation in relation to "soft" information last September.
"This legislation has been prioritised by the Minister for Children and Youth Affairs and is currently being worked on," the spokeswoman said.
The development came as Catholic primate Cardinal Seán Brady reminded bishops, in a strongly worded statement, of "the moral and civic duty on everyone with responsibility for safeguarding children to implement all statutory guidelines" on reporting allegations of abuse and on working in full co-operation with the relevant statutory authorities.