The head of the HSE has called failings within the South Kerry Child and Adolescent Mental Health Services "completely wrong".
A report published in January found that 46 children suffered "significant harm" while attending the service.
The terms for an audit of services are currently being drawn up.
Appearing before the Public Accounts Committee, Paul Reid rejected claims that the whistleblower has been mistreated, saying he has written to Dr Ankur Sharma to thank him.
"I have written to Dr Sharma on the 17th of February and thanked him for what he had done - for what he had highlighted", Mr Reid told the Public Accounts Committee.
"Dr Sharma wrote to me on the 25th of February" under a protected disclosure which must now be respected, he said.
"That is now in a formal process. We are now engaged with Dr Sharma in terms of how that process will proceed. And we will investigate all issues outlined by Dr Sharma in his protective disclosure," Mr Reid added.
Mr Reid said that an independent investigator is being appointed to examine claims submitted under protective disclosure by Dr Sharma.
Dr Sharma sparked a review into mental health services for young patients and has since spoken of being sidelined by the HSE as a result of his whistle-blowing.
Asked by Sinn Féin Deputy Imelda Munster if it is "standard practice" to punish or sideline whistle blowers, Mr Reid replied: "Absolutely not. We have very clear procedures, guidelines, quite thorough procedures" which "clearly set out that's exactly the case what shouldn't happen - nobody should be punished".
"That is not a policy, and I have no experience of a person being punished for it," he added.
"We are appointing an independent person - an authorised person - to [investigate Dr Sharma's claims] under the [2014] act", he said.
Paul Reid confirmed that Dr Scharma has left the HSE.
What happened was a 'complete failure'
Mr Reid condemned what had happened at South Kerry CAMHS as "a complete failure in terms of governance, in terms of clinical oversight, in terms of general administration, in terms of supports, in terms of risk management".
He told Deputy Imelda Munster that his teams are "working through with the minister on the full details of the scope of the audit and other initiatives based on Dr Maskey's report".
It will be a full audit across all the CAMHS teams, he added.
Sinn Féin's Matt Carthy said that Mr Reid had given "a very frank and honest assessment" of what had happened in CAMHS.
He asked the Chief Operations Officer at the HSE if she is satisfied "that there are now measures in place that would prevent similar things happening again".
"Can I say for sure that there will never be instances in services again? Absolutely not, I would never say that in terms of health services," Anne O'Connor said.
However, she added that what had happened was "very specific in one area" and "not about a generalised issue".
Ms O'Connor said the audit would be "looking in depth at ADHD prescribing".
She added that Minister of State Mary Butler has asked for a "look at broader prescribing practices, and we are now finalising how we will do that".
She said she could not say when the review would begin, whether in "March or early April".
Mr Carthy asked if Minister for Health Stephen Donnelly had only been told of the problems when the Maskey Report was finalised, just "months before" its publication on 26 January, 2022.
Yvonne O'Neill, Head of Service Mental Health at the HSE, said that "we would have been advising the minister from when it was available to us in draft".
Labour TD Seán Sherlock pointed to a reply to a parliamentary question he had tabled.
3,357 people waiting for CAHMS appointments
It said that 3,357 are people waiting for CAHMS appointments.
Ms O'Connor said that half of those were under the 12-week target time, but accepted that 1,700 of them had waited more than three months.
Urgent cases are triaged and processed within three days, she said.
Overall, 9,554 young people are waiting for appointments across all psychology services, Mr Sherlock said.
