The woman who carried out a Health Service Executive audit on the St John of God organisation has said the findings are shocking.
The audit found the charity had not complied with public pay policy for over 30 years, and that there had been confidential arrangements and a private payroll system.
Speaking on RTÉ’s News at One, Dr Geraldine Smith said the audit identified significant private payments to senior management, "payments that ranged from €23,000 to €107,000 per annum".
She said the audit identified that these payments went as far back as 1986.
Dr Smith said the HSE engaged with St John of God in March 2013 to bring it into compliance and it had to declare any over payments.
She said the order was not straight with the HSE.
Dr Smith also said she does not accept the statement issued by the order that the payments were made in good faith.
Earlier, the organisation warned that a draft review by the HSE will take a very critical view of payments made to managers in 2013 and other non-compliances with public pay policy.
However, the order said that the payments were made in good faith following independent professional advice received by the organisation to discharge a possible future pension liability.
It said it did not believe that it deliberately misled the HSE at any point.
The Irish Times reported today that a confidential HSE audit uncovered secret payments totalling €6.24m to senior lay executives.
It also said the organisation made €1.85m in undisclosed payments to senior managers after being instructed by the Vatican to deal with outstanding liabilities.
In a statement, St John of God said that as it is in active dialogue with the HSE about the review, it is not appropriate to comment in any detail pending the finalisation and publication of the review.
It said it has co-operated fully with the HSE in the course of the review process and is committed to working with the HSE in the period ahead, concerning the resolution of outstanding issues.
It continued: "This matter has gone on for a considerable period and the order along with Community Services is keen to move forward.
"We welcome the publication of the review once it is finalised. The Board of Saint John of God Community Services is committed to and has already established a group to review and develop governance systems to ensure that the service operates in accordance with the required legislation and regulation. This includes compliance with public pay policy."
The order also pointed out that it provides services to over 8,000 children and adults in centres around Ireland, with a range of needs including intellectual disability, mental health difficulties and problems associated with getting older.
Since 2013, the order said it has provided direct funding in the amount of €16 million, in support of the work of community services.
The Minister of State with responsibility for disability services has appealed for St John God's Services and the HSE to be given the space to bring their discussions on the HSE audit of pay in the charity to a conclusion.
A spokesperson for Minister Finian McGrath told RTÉ News he understands that the final audit report is soon to be completed and, in line with due process, the minister has not seen the HSE's draft report.
RTÉ News understands that a final report is expected within 11 days.
The minister's spokesperson said Mr McGrath is aware that the HSE and the charity are also involved in an external review to examine governance arrangements in voluntary providers of State services to people with disabilities and that progress is ongoing on both fronts.
The spokesperson added that, as far as the minister is concerned, when taxpayers' money is allocated to disability services, the highest standards of governance are expected.
