The omitted section was the only part of the questionnaire labelled “audit”.

In May 2007 the Health Service Executive informed the Office of the Minister for Children that Section 5 of the audit had caused difficulty.

It was decided to proceed without it.

This part of the questionnaire asked how previous cases had been dealt with and if guidelines were followed.

In late 2006 some dioceses indicated they had no problem answering section 5, but asked for clarification.

Others feared it compromised a person’s right to a good name and presented “insurmountable difficulties”.

The section did not ask for names of offenders but queried each bishop’s role in forwarding on the complaints to the relevant authorities.

The questions would have only compromised the good name of the bishops themselves.

Other sections dealt with present practices and hypothetical commitments.

By allowing dioceses not to answer section 5, Bishop of Cloyne John Magee was able to sign the audit in January 2007 without admitting his failure to follow church or state guidelines.

This would not have emerged without separate allegations coming from One in Four, nine months later.

Both the Dublin Rape Crisis Centre and the Children’s Rights Alliance last night asked for an explanation from the Minister for Children Barry Andrews and the HSE.

Despite the difficulties some dioceses filled in the section regardless, others did so partially. Ferns diocese has said it had no legal problems.

However, in May 2007 Chief executive of the HSE, Brendan Drumm said the majority of bishops had highlighted problems. He suggested the uniformity of responses meant they were acting in concert.

“Whilst not explicitly saying so, the similarities in the bishops’ individual correspondence implied that their stance was based on collective legal advice,” he said.

The HSE obtained its own legal advice and this was sent as an attachment to Prof Drumm’s letter.

Last night, the Catholic Communications Office spokesman Martin Long said the HSE never came back to the bishops with a solution and the audit progressed regardless.

At the end of Prof Drumm’s May 2007 letter he said he would update the then children’s minister Brian Lenihan of any developments with Section 5. Such updates were not included with yesterday’s audit.

Prof Drumm told Mr Lenihan it continued with the audit regardless, though this meant it was impossible to examine the application of the procedures in dioceses.

The result was furnished to the minster’s office 12 months ago when it was indicated the audit was complete, but that Cloyne was taken as a separate issue.

The victims’ groups have said the manner in which the Cloyne diocese was able to evade the audit had compromised the entire process.

Before Bishop Magee sent his response to the HSE in January 2007 he would have had the option to outline his actions with previous allegations and state specifically if he asked the HSE.

It would have asked Bishop Magee “had all complaints or allegations of child sexual abuse made to the diocese been brought to the attention of the HSE and the Garda Síochána”.

The National Board for Safeguarding Children in the Catholic Church (NBSCCC) report has since revealed he did not refer allegations to the HSE and, as another question in Section 5 asked, or pass on details to the gardaí at the earliest possible opportunity.

There was no way of knowing how many other bishops have dealt with allegations, removed priests from their work or handled information on abuse and also skipped over the section asking them to account for their actions.

Mr Andrews said the lack of information from Section 5 was a disappointment.

“In an attempt to overcome this difficulty, my office and the HSE will be engaging with the NBSCCC over the course of the next few weeks to explore and put in place mechanisms that will ensure that both the HSE and the NBSCCC can be satisfied that the highest standards of child safeguarding will be implemented,” he said.

But the section’s expected absence was flagged in the May 2007 letter. This was not acted upon.

However, it is still unclear as to why the bishops did not respond to section 5 when it did not ask for specific names. Or why the HSE accepted the audits without pressing the need for explanations on how dioceses dealt with previous allegations.

And if the department knew in May 2007 Section 5 was causing a problem, why did it not act on alternative options outlined by Prof Drumm’s legal team.