The Health Service Executive today apologised to survivors of child sexual abuse for the shortcomings of the health boards in dealing with victims.
The HSE said it recognised the need to strengthen its childcare data management, and had already begun to introduce a standardised system of referral and assessment throughout the four HSE regions.
"This new system will see a standardised approach being applied for the collation of data in respect of child abuse allegations," the HSE said in a statement.
The new system is due to commence in January.
The organisation said it had made every effort to comply with the commission during its investigation of the allegations of abuse, but said this was affected by data management systems in place in the HSE.
"Some difficulties arose due to the fact that the HSE collates child protection data per child while the Commission requested data on alleged perpetrators. This hindered the response process as a considerable amount of cross-referencing of files was required," the HSE said.
"The fact that there were different methods of collecting and recording data across the health system also impacted on the search process and subsequent responses to the commission."
The HSE said its National Counselling Service, which is available free of charge for adults who had experienced abuse, had been extended in light of the report. It had already received 50 calls throughout the day, it said. and other agencies were also reporting a large number of calls.
The HSE said its questionnaire audit of the Catholic Church's child protection polices and practices is nearing completion. The report is expected to be presented to the Minister for Children and Youth Affairs early next year.
"In addition to this, the HSE will be seeking to meet with the National Board to ensure that there are appropriate systems in place in the Catholic Church in Ireland to ensure that robust safeguarding structures are in place to ensure the well being of children," it said.