Many parents of special needs are 'disgusted' with the fact that the Central Remedial Clinic used charity donations to fund top-up payments for well-paid staff members.
The CRC is separately under fire for their pensions scheme.
Chair of the Special Needs Parents Association Lorraine Dempsey explained that many donors would be 'pulling the plug' on their charitable donations for fear that the funds would be misappropriated.
"We already know parents who are connected with the CRC who would have been involved with fundraising through their annual Santa bear appeal and they're now pulling the plug on their support because they're looking at, 'Is it a top-up to a CEOs salary' or is it for their own family."
Similarly, Minister for Public Expenditure and Reform Brendan Howlin explained the obstacles necessary to overcome in order to address top-up payments as a whole in the public health sector.
"With great difficulty is the honest answer," he told Morning Ireland, when quizzed about how the Government planned to tackle the top-up payment
"I'm a former Health Minister and I know the way our health services have developed over time is that we do franchise work to private companies in terms of voluntary companies incorporate dinto company law.
"They are their own governing structures, accounting bodies and accounting officers. To actually have transparaceny across everyone who has public money has been one of my ambitions for the last two and a half years, but we're unravelling decades of practice.
"Even the efforts of the HSE to get data from some of these agencies wasn't responded to until the internal audit unit of the HSE was tasked with the job and drilled down. Now we have a report that I think lays out, for the firs time, how extensive these top-up payments are. But they're not all the same.
"They're coming from different source,s some are contractual arrangements, some are just downright top-ups.
"We have to find out who is breaking the rules.
"This is primarily a matter of the HSE, they have a contractual arrangement with each of the agencies and bodies and it needs to be clear what , if the terms, are of each contractual arrangement. Does it allow, for example, the individuals to have alternative sources of income - in some, that is the case. It's not one common phenomenon, that's what makes this both complicated and difficult."
The 'top-up' funds were raised by a separate company called the Friends and Supporters of the Central Remedial Clinic.
The CRC said the money contained in the fund is generated from a share of the operation of a lottery.
It was claimed the Central Remedial Clinic (CRC) received a €3m interest-free loan from its fundraising arm to help prop up pensions, despite the clinic having to impose cuts in services.
Independent TD Shane Ross claimed the Friends and Supporters of the Central Remedial Clinic -- which had funds of €14m in 2011 -- gave the CRC's private pension scheme the financial lift last year.
He insisted the €3m loan to the CRC would be better termed a "gift" and described it as "devastating".
It earlier emerged that charity money raised through the Friends and Supporters of the Central Remedial Clinic was also used to fund generous top-ups to well-paid managers.
The clinic, which receives €19m from the HSE, is the first disability organisation which has admitted it is using charity funds to pay for salary extras.
Former CRC chief executive Paul Kiely, who got €136,000 from the charity fund before his recent retirement, was also on a state salary of €106,900.
Mr Kiely had also been secretary of the Friends and Supporters group.
A spokeswoman for the Central Remedial Clinic said five managers, who have not been named, continue to be paid an extra €32,000 each on top of their state salaries.
These salaries were all above €100,000 before the recent Haddington Road Agreement cuts.
Mr Ross said the board of the CRC should resign as a result of the revelations.
"It is obvious people are being deceived about where their money is going. It is a voluntary organisation and the money should be going to sick children but it is being diverted to It was sitting on €14m in 2011 - a figure which has grown by €5m since 2008 at a time when most charities have seen a squeeze in public giving.
Friends and Supporters raises funds including a share from the operation of a lottery, administered by the Care Trust, which also funds the Mater Hospital.
It does not receive any funding from the National Lottery however.
Many who contributed to the Friends and Supporters fund over the years would be shocked to find out that part of the money was going towards extra payments for managers at the clinic.
Asked to comment on the controversy over top ups, the head of the Disability Federation of Ireland John Dolan said he was reserving judgment at this stage.
Questioned on whether he feared that this will lead to a reduction in public donations, he said :"It is not good for public confidence and could lead to people not supporting organisations at a time of cutbacks."
A spokeswoman for the Central Remedial Clinic said: "Friends and Supporters enables the Central Remedial Clinic to fund a number of large capital projects. These have included the development of CRC Waterford, a large state of the art centre which provides services to children with physical disabilities in the South East region, at a cost of €2m."
It also funded a large renovation projects at CRC Clontarf, at a cost in excess of €7m since 2004. It also funded the development of CRC Limerick, a clinic which provides a range of specialised services for the Mid-West Region.
She said in 2009 the Central Remedial Clinic had an agreed position with the HSE to phase out the level of management salaries being paid, over and above the Department of Health's consolidated pay scales.
"Nine posts were identified in correspondence with the HSE. It was agreed at the time that as these positions became available through retirement or vacancy, new staff would be engaged on compliant salaries," she said.
"At present only five of these posts remain following retirement and vacancy and two of these posts are due to retire in the next two years.
"In line with this agreement, the salary of the Central Remedial Clinic's new chief executive, Brian Conlan, is fully compliant. "
She said that Friends and Supporters continues to support large scale capital projects at the Central Remedial Clinic.
Funds are earmarked to build a new state of the art centre at CRC Clondalkin and a new day activity centre for adults in Swords, which is in discussion with the HSE at the moment. Projected costs for these projects are estimated in excess of €9m.
The current directors of the Friends of and Supporters wing includes the new chief executive of the Central Remedical Clinic Brian Conlan; James Nugent, a long time Fianna Fail supporter; Hamilton Goulding, son of the late Lady Valerie Goulding; Hassia Jameson and Ailbhe Rice. They are not in receipt of top-ups.
The the directors of the fund raising charity are also on the board of the Central Remedical Clinic.
Eilish O'Regan Health Correspondent