It has emerged that charitable funds raised by Friends and Supporters of the Central Remedial Clinic (CRC) were used to pay top ups to managers at the company.
In a statement this afternoon, the CRC said some money from the fund was used to pay executives over and above the pay scales of the Department of Health.
But the CRC says it told the Health Service Executive (HSE) it would phase out the top ups in 2009.
It says "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. 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".
It also says that in line with this agreement, the salary of the its new Chief Executive - Brian Conlan - is fully compliant.
The Central Remedial Clinic is a non-residential national centre for the care, treatment and development of children and adults with physical disabilities - such as cerebral palsy, spina bifida, muscular dystrophy and arthrogryposis.
In 2001, the CRC opened a centre in Waterford to service the south-east region.
Independent TD for Dublin South Shane Ross has called for the immediate resignation of the board of directors, as the CRC was using charitable funds at a time when it was cutting services for children and adults with physical disabilities.