The chief executive of the scandal-struck Central Remedial Clinic has insisted his successor should have no previous links with the hospital.
Brian Conlon said he stood down in the wake of the top-up payments controversy to allow the clinic start afresh amid public outrage at executive bonuses.
"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," he said.
Mr Conlon, who has only been in the top role since the summer and whose appointment has come under scrutiny recently, insisted his own pay was within health service guidelines.
"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 added.
"I hope that the CRC will now take the opportunity to start afresh with a clean slate so that the excellent service provided by its dedicated staff can continue to be made available to its clients who rely on it and who should not be the innocent victims of any fallout."
Mr Conlon resigned after revelations that public donations were being used to top up the salaries of bosses at the centre, which treats adults and children with physical disabilities.
The CRC had been dipping into funds raised by a company called Friends and Supporters of the Central Remedial Clinic to boost pay packets of top executives.
The disclosure sparked furore among donors and relatives of those who rely on the clinic for their medical needs.
Mr Conlon said he was abroad on holidays at the time, but tendered his resignation within a day of coming home.
Despite his calls for a clean break with past leadership, Jim Nugent, chairman of the board, is standing in as chief executive on an interim basis.
Education Minister Ruairi Quinn has called for the entire board of directors at the CRC to resign.
In a statement, the board of the CRC confirmed it accepted "with regret" the resignation of Mr Conlon with immediate effect and thanked him for his service. Mr Conlon was a former member of the board.
It was also announced that Joan Hurley will become operations director in the day-to-day management of the clinic and will co-ordinate the senior management team.
"The board will work closely with the senior management team and staff to ensure a positive future for the CRC, its service users and staff," the statement added.
But Labour Party TD Robert Dowds, a former special needs teacher in a CRC school, said the rest of the board should resign unless they can defend their own role in the controversy.
"The CRC has a lot of questions to answer about what was going on in this matter, and, to my mind, they have yet to answer them satisfactorily," he said.
"After today's resignation by the chief executive, I think the rest of the board need to answer these questions satisfactorily before the Public Accounts Committee next week or else they too should resign."
Mr Dowds said he was alarmed at revelations that well-paid bosses in the clinic were getting massive bonuses from public donations on top of already large salaries.
"There are also questions about the 14 million euro (£11.7 million) fund which the CRC has built up in a separate account, and answers need to be given about what that money is for," he added.
"Given that the CRC depends on charitable donations and is also funded by the taxpayer, this raises huge questions about the CRC.
"I want the rest of the board of the CRC to answer these questions satisfactorily.
"If they cannot do that, then for the good of the people who depend on the services of the CRC, they should all resign."