A confidential HSE report shows a number of managers are receiving contributions equal to half their salary, far higher than normal employer contributions.
The report, which has been seen by Health Minister James Reilly, said the "continued payment of public funds into private pension schemes is of concern".
It can also be revealed that 12 senior hospital executives have each been receiving gold-plated private health insurance of up to €5,300 a year, despite their leading roles in the public health system.
Last week, the Master of the National Maternity Hospital Dr Rhona Mahony said she had been "vilified" after it emerged she received a number of additional payments on top of her basic salary of €182,000.
Yet, today we uncover the true scale of the top-ups and allowances enjoyed by a coterie of 191 senior health executives in our leading hospitals and care centres.
A significant proportion of the controversial allowances paid every year are unauthorised and granted without any HSE/departmental sanction, and many managers are in receipt of more than one top-up on top of their salaries.
Also, a number of hospitals repeatedly refused to disclose salary and allowance details requested by the HSE audit department, the report states.
* In total, €3,223,950 was paid out annually to 191 managers in allowances out of HSE funds. In addition, €912,472 was paid out to 34 managers in salary and allowance top-ups from private funds.
* One Dublin teaching hospital (which we have confirmed to be the Mater Hospital) paid €25,625 in additional remuneration to its CEO Brian Conlon, in "respect of the hospital's development programme". The Mater boss also gets €3,500 in a car expenses allowance. The Department of Health said that no documents in which approval is given for such payments exist in their records.
* €173,000 was paid to 17 managers in undisclosed allowances. "Agencies did not provide the title of the allowances," the report said.
* Two executives in Our Lady's Children Hospital were paid €53,065 extra for taking on additional management duties.
* Two managers in St James's Hospital received two top-up allowances for assuming extra duties.
* Four senior executives in the Royal Victoria Eye and Ear hospital were paid €89,415 as a contribution to the Hospital Management Group.
* One executive from Our Lady's Hospice received €12,700 to manage another location.
* One senior figure at St James's Hospital received a post-graduate co-ordinator allowance of €51,617; the Hospital's Haemophilia unit director got €43,468 in a top up; while the hospital's director of clinical audit unit got €36,417 on top of their salary.
* Four senior managers at the Dublin Dental Hospital got €86,400 in external on-call allowances.
* One manager at Our Lady's Children Hospital got a €27,931 allowance for advising on 'clinical risk'.
* One hospital said allowances paid to 26 managers were done so in accordance with Department of Health guidelines but the department disputed that claim saying "no records were found in relation to agency/hospital approved allowances or for any of the allowances listed for the 26 senior management posts".
* In total, 14 managers in four hospitals had part of their salary paid for out of private funds at a cost of €409,631, or €29,259 each. St Vincent's Hospital Dublin failed to disclose how much it was paying in salary top-ups out of private funds.
* Of the privately funded allowances, 23 of the 34 managers identified receive one type of top-up payment, 10 receive two types and one manager received three types.
* €396,376 in private funds was used to pay allowances to 18 managers in the following hospitals – the Coombe (one manager), the Mater (one), Holles Street (four), National Rehabilitation Hospital (one), Rotunda (five), South Infirmary (one), CRC (one), Our Lady's Hospice (three), Our Lady's Children Hospital (one).
In relation to the use of taxpayers' money to fund private pension contributions for 29 managers in nine hospitals, the report said the practice has continued despite six of the nine hospitals being covered by the public sector pension scheme.
"The rate of pension contributions from public funds to these private pension funds by these agencies range from six per cent to 46 per cent of salary," the report revealed. Some of the centres involved include Brothers and Sisters of Charity institutions throughout Ireland.
While some of the allowances are deemed to be legitimate, Dr Smith determined that both salaries and allowances were paid without proper sanction from either the HSE or the Department of Health.
"There is no current arrangement in place whereby employers are authorised to supplement the approved rate for any post, senior or otherwise," the report said.
She also concluded that where senior managers' pay differed from consolidated salary scales, hospitals and agencies said they relied on "verbal approval" from the Department of Health which was given.
However, having checked, the report concluded that no documentation of such agreements exist in Department of Health files.
Five senior executives at the Stewarts Hospital for the disabled are in receipt of up to €5,347 in private health insurance top-ups every year.
The audit report also stated hospitals in various regions either refused or repeatedly failed to disclose properly the full extent of the payments to senior managers.
The report concluded that "there is no current arrangement in place whereby employers are authorised to supplement the approved rate for any post, senior or otherwise".
Dr Smith added that the Department of Health "had not located any papers dealing with the terms and conditions of existing individual CEOs or senior post holders in these Section 38 agencies".
It is also reported that 34 of 63 disability service providers who receive HSE and other funds confirmed that the pay of their CEOs was in excess of stated HSE rules, with 13 of those bodies saying the breach in the pay scales exceeded 15 per cent.
Crucially, the report determined that financial emergency legislation introduced by the Government requires all public sector bodies to recoup any salaries paid which are not in accordance with approved public sector rates.
However, Dr Smith's audit concludes "no system yet exists within the HSE to retrieve such overpayments".
On foot of her investigations, Dr Smith made 22 key recommendations in her report.
* A clear need for health sector allowances to be reviewed, rationalised and for a definitive list of allowances to be issued.
* All non-standard allowances must be fully sanctioned by the HSE/Department of Health and should be regularly reviewed.
* Discussions between the Department of Health and hospitals should conclude "as soon as possible" in order to end the payments of public funds into private pension schemes.
* Pay rates of CEOs "do not necessarily reflect the comparable size, scale and complexity of each organisation today". All salaries should be reviewed immediately.
* All future appointments to CEO or senior management posts should require sanction to approve the entirety of the remuneration package and any deviation must have approval.
* The HSE must develop a proper system of recouping unsanctioned or excess payments.
* It also said there must be a "clear and unambiguous policy on the issue of providing additional remuneration to senior managers from private sources".