The HSE and Childrens Health Ireland have acknowledged distress experienced by children with spina bifida and scoliosis, and their families.
It follows a review of care at Temple Street Hospital in Dublin.
In a statement issued last night they also apologise for unacceptably long waiting lists for surgery.
HSE chiefs ordered a review into spina bifida paediatric care at the hospital after one child died and others suffered serious catastrophic complications after surgery.
It was established that children who received a particular spinal surgery in the hospital had to return to the operating theatre 11 separate times on average, with one child returning on 33 occasions.
The Minister for Health confirmed that Clinicians raised concerns about the Temple Street scandal a year ago.
Stephen Donnelly said professionals should have felt safe and secure in making such a report, which did not happen in this case and the review would look at why.