Central Remedial Clinic Chief Executive Brian Conlon has resigned following the controversy over top-up payments at the organisation.
Mr Conlon took up the post in July of this year, having previously been chief executive of the Mater Hospital.
In a statement his afternoon, Mr Conlon said he was away on leave when the controversy started.
"Within 24 hours of returning to Ireland I tendered my resignation with immediate effect," he said.
"I believe that it is in the best interests of the Central Remedial Clinic's clients and staff that the new chief executive should not have any association with legacy matters at the CRC."
Mr Conlon said his salary was within the guidelines provided by the HSE.
He said he hopes the CRC can "start afresh with a clean slate" following his resignation.
"I believe that there should be full transparency within the charitable sector with regard to how all funds raised, both private and public, are spent and that all executive remuneration should be within HSE guidelines," he said.
In November, the CRC confirmed that some of the money donated by the public was being used to top up the salaries of some of its staff.
The funds were raised by a separate company called Friends and Supporters of the Central Remedial Clinic.
The CRC admitted the additional salary amounts were over the Department of Health's consolidated pay scales.
In a statement this afternoon, the board of the CRC confirmed it had accepted Mr Conlon's resignation.
Chairman Jim Nugent has been appointed interim-CEO.
Joan Hurley will take over the day-to-day management of the clinic and will coordinate the senior management team as Operations Director.
Conlon will not appear at PAC meeting
It was confirmed this evening that Mr Conlon will not appear before the Public Accounts Committee on Wednesday when it discusses the top-up controversy.
A spokesperson for Mr Conlon said he will not be attending as he has now resigned.
He said he has no information that is not known by the remaining officers and directors of the CRC.
Earlier, PAC Chairman John McGuinness said it would be extremely helpful to the investigation if previous chief executive Paul Kiely and Mr Conlon were to come before a special sitting of the committee and explain the matter of pay in detail.
Speaking on RTÉ's Six One News, Mr McGuinness said he thought it was hugely important for the CRC and for the sector that both individuals and the board come forward in order to allay public disquiet.
He said the committee would need to see the paper trail on Wednesday morning as to what meetings were held and what authority was given to the CRC, if any.
He said someone made a decision to give the top-up payments.
Taoiseach Enda Kenny also said earlier that he expected Mr Conlon to appear before the PAC.
Speaking on RTÉ’s Prime Time tonight, independent TD Shane Ross, a member of the PAC, said it was "an extraordinary decision" by Mr Conlon not to appear before the committee.
Mr Ross said he would ask the PAC to look for compulsory powers to bring Mr Conlon in.
Mr Ross earlier said there may be more resignations to come after Mr Conlon's decision to step down.
Speaking on RTÉ's Today with Sean O'Rourke, Mr Ross said the appointment of any successor should not be supervised by the current board. Mr Ross said it should be advertised and selected externally.
He said he hoped that by the time a successor is appointed the members of the board would have stepped down.
Mr Ross said anybody who was involved in the appointment of Mr Conlon, or in authorising top-ups for Mr Kiely, should not be involved in any way in the new appointment.
He said the Health Service Executive may have to take a hands-on role in the appointment of a successor to Mr Conlon.
Elsewhere, Sinn Féin deputy leader Mary Lou McDonald called on Minister for Health James Reilly to intervene in the controversy.
The HSE said the resignation was a matter for the CRC.
A spokesperson said the executive remains in discussions with 'Section 38' voluntary agencies in order to ascertain degrees of compliance with public sector pay policy.
He said the HSE continues to receive documentary proof of compliance.
The spokesman said the Director General of the HSE has commenced meetings with the chairpersons of voluntary agencies.
He said that process will continue over the next number of months.