During the Emergence hearings, Sr Breege O’Neill, then Congregation Leader of the Sisters of Mercy, outlined the organisational structure of the Congregation: At that time  she [Catherine McAuley] was very clear that for us to be able to be about that work it was important that we would be locally based, and that we would not be constrained by central Government ... It emerged within 20 years of her founding the first house of the Order in Baggot Street. There were convents established in each of the 26 diocese in Ireland ... In some there might have been eight or nine convents ... These convents were autonomous. They were totally, completely and entirely responsible for their own affairs really. There was little central or there was not a coordinating structure among the convents ... there was not a sort of a central Government that established these, but they were established in each locality according to the need of the locality at the time.
On 1st July 2004, Sr Breege O’Neill, Leader of the Congregation, gave evidence to the Investigation Committee held in public on behalf of the Sisters of Mercy dealing with the emergence of allegations of child abuse in the Sisters of Mercy institutions. She spoke of the great hurt felt by the Community at the allegations that were being made, and also spoke of the enormous sacrifice made by Sisters throughout the years in aiding the poor and needy in this country. She asked that a proper and balanced investigation should take place into this whole matter.
The issue of sexual abuse did not feature as prominently in the evidence in relation to schools run by the Sisters of Mercy as it did in relation to schools run by other religious communities. There were, however, some very serious incidents of sexual abuse perpetrated by lay staff in some schools, which are dealt with in the individual chapters. During the Emergence hearings, Sr Breege O’Neill stated that the Congregation became aware of a small number of complaints from the Leadership’s discussions with Sisters who were involved in the industrial schools. She stated: I am aware of, I think, three, if not four ... Let me mention that there were three instances where the Resident Manager in a particular institution became aware of a concern that sexual abuse might have occurred in relation to a child. I am talking about an instance in 1960, one in the mid 60s and one in 1969. They were instances where that came to the attention of the Resident Manager and the individual Manager took action herself in relation to each of those three cases that we are aware of. One was in relation to somebody who was visiting the Institution and she barred that person. She mentioned it subsequently to a Department official. The other one was in relation to somebody who was working in a maintenance capacity. Again the Sister had that man removed. The third one was a volunteer coming in and when the Sister heard the complaint she sent for him but he never came back to the Institution. That would be from the recollection of the Sisters themselves ... Some of that, the dismissal, we have found some records that substantiate that.