Taoiseach Enda Kenny has warned hospitals and health agencies that executive pay must not breach a salary cap.
As a deadline loomed for information on wages, it has been revealed that just seven out of 44 institutions have confirmed they are in compliance with pay scales for senior managers, with 13 admitting non-compliance.
"We can't have a situation where clearly those on higher levels in these areas are in receipt of what are allowances that are outside the agreed public pay service scale," the Taoiseach said.
He said public pay service agreements should not and cannot be breached by unapproved non-exchequer payments.
"We cannot have a situation where those further down the line, who have taken serious change in the restructuring of the health system, have borne the brunt of the situation, (and) where we now find that some people appear to have received non exchequer top-up payments which, in some cases, amount to more than the basic salaries of those further down," said Mr Kenny.
Health Minister James Reilly ordered an audit after the health watchdog, Hiqa, found a senior manager at Tallaght Hospital has been paid an additional 150,000 euro in payments since 2005.
Mr Kenny said the Health Service Executive (HSE) has twice written to the 44 voluntary hospitals and disability agencies demanding to know the wages and allowances of its most senior staff.
The deadline for written replies was the end of today.
The letters sent to the non-HSE run facilities also warned salary scales must be strictly adhered to in the future.
Mr Kenny said all agencies must respond fully to the HSE's request for information so a full report can be published and discussed by the Oireachtas committee on health.
Health Minister Dr James Reilly warned that further action will be taken against hospitals and agencies that are not compliant with the public service pay policy.
"Clearly there may be some situations where there is extenuating circumstances or a particular business case can be made," he said.
"I can't foresee all the eventualities but the HSE will examine them and report them to me. And if people aren't compliant at that point then further action will have to be taken."
"Agencies and hospitals get the same pay and conditions as all public servants, they get all that goes with that and therefore we expect and it is Government policy that they will also be subject to public pay policy and conditions.
"That's the quid pro quo and they can't have it both ways."
The minister added: "We're all in the same boat here. This country is starting to get back on its feet. It's succeeding to do so. A lot of people have taken pain. In my view and the Government's view, everybody should share the gain, not just the few."
Figures have revealed a quarter of health agencies or hospitals have overpaid its senior managers and medics, breaching public service pay agreements.
Department of Health files dated from May this year showed Master of the Rotunda Hospital, Dr Sam Coulter Smith, was on 306,000 euro, including a HSE salary of 236,000 euro, 49,545 euro on-call allowance, and a 20,000 euro top-up from the hospital's private funds.
Other senior staff at the Rotunda were also receiving additional allowances from the private fund, ranging from 6,000 euro to 17,000 euro.
Private funds of 45,000 euro were paid to Dr Rhona Mahony, master of the National Maternity Hospital, bringing her pay up to 281,000 euro.
The Central Remedial Clinic in Dublin, which has a range of services for children and adults with physical disabilities, was paying its chief executive Paul Kiely more than 240,000 euro, well above his HSE-funded salary of 106,900 euro.