The report revealed how the HSE only filed child abuse reports under the name of the victim and not the alleged abuser, which forced staff to go through each file manually.
A spokesman for the HSE said yesterday a new database will be set up in January, allowing it to locate the name of the alleged abuser more quickly if it is asked to produce a file.
However, the system will not be retrospective, meaning that any attempt to find existing files must be done manually.
The HSE told the commission in 2006 that it had more than 114,00 child abuse files, each of which would take a half a day to look at, or a total of 10 years to get through them all.
The spokesman said: "The HSE has learned from its response to the commission in relation to the Dublin archdiocese and improved its processes in responding to the commission for Cloyne."
The HSE will continue to file the records under the name of the victim -- but the new system will give it the ability to also search by the name of the alleged perpetrator for all new cases from January.
Meanwhile, the commission found that the health authorities had relatively little involvement in complaints made before the mid-1990s.
The former Eastern Health Board was involved in the case of Fr Thomas Naughton in 1988 and this was one of the the "few cases examined in which the health board personnel took a proactive role in trying to prevent abuse".
The commission pointed to the constraints of resources and inadequate legislation which hampered health authorities.
It warned: "The law at present does not provide adequate powers to the health authorities to promote the welfare of children who are abused or in danger of being abused by people outside the family and in particular by people who have privileged access to children."
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