A quarter of the country's State-funded hospitals and health agencies are in breach of policy guidelines on pay for senior staff.
In some cases top executives are paid well over €200,000 a year.
Figures released by the Department of Health show that salaries are made up of HSE-funded payments and topped up with funds from private sources such as the proceeds of the on-site shops and parking.
These figures show that one in four of the country's 43 hospitals and health agencies are in breach of policy guidelines on pay.
For example the Master of Holles Street is paid a salary of €236,000 which is topped up with private funds of €45,000.
Holles Streeet is among a number of voluntary organisations paying generous allowances from private funds and it is also one of a number of hospitals having difficulty balancing the books.
The Department of Health said its policy is that non-Exchequer sources of funding cannot be used to supplement approved rates of remuneration.
The HSE has written to the 43 agencies asking them to confirm compliance.
So far five say they have stopped the payments, with 10 others asking for more time to examine legal and contractual issues.