Paul Reid apologised on Thursday, in the wake of a damning review of mental health services in Co Kerry.
A review of the care of more than 1,300 children who went to the South Kerry Camhs found that 46 children suffered significant harm.
The HSE report found that hundreds of children received “risky” treatment at the hands of a doctor working in the service.
The review of the young people who attended the mental health services found that the 46 children suffered significant harm, lethargy, distress, raised blood pressure, significant weight gain and the production of breast milk.
Concerns raised about the doctor, who is not named in the report, sparked a review of the services.
Taoiseach Micheal Martin told the Dail on Wednesday that the findings demand a “fundamental review” of child and adolescent mental health services.
Mr Reid, speaking at a HSE briefing on Thursday, called the findings of the review “deeply regrettable”, “beyond comprehension” and “just so wrong”.
“The report very clearly demonstrates some of the basic clinical oversight and prescription processes and general management processes were at least lacking and if not in some cases abandoned.
“This no doubt had a very significant impact on many children, which the report sets out and indeed on many of their families and none of us can bear to how we might feel if one of those were our children who went through what some of these families and children have had to go through.
“So as CEO, I certainly want to sincerely apologise for what had happened over a sustained period of time in this service in this area.
“We do value the public’s trust and confidence in our services and there’s no doubt what occurred in this instance and in this service severely impacts that trust and confidence.
“I do want to reassure that the team we have in place there now, the executive clinical director and the community officer are highly committed and fully embracing all aspects and all elements of the recommendations as set out in the report.”
In the Dail on Wednesday the Taoiseach described the report as a “profoundly serious issue”.
“I have read the executive summary of the report, it is shocking and very serious,” Mr Martin said.
“What happened is unacceptable.
“It represents a damning indictment of the service.
“The first principle of medicine is to do no harm.
“Children were harmed here by a complete failure of clinical performance and oversight and by the entire management of the service.”