The HSE has ordered almost 30 hospitals and clinics to stop paying top-ups to senior managers.
It has written to the Section 38 agencies telling them that there is no justification for the extra payments that bring them above the public-sector pay limits.
In a report to the Public Accounts Committee (PAC), the HSE said that more than 130 staff are to lose the allowances in July.
It is up to the individual employer to enforce the cut, however.
Labour TD and PAC member Gerard Nash says the employers know there are major consequences if they do not follow through.
"Well, ultimately the sanction that the HSE has is to withdraw levels of funding to these organisations, so the organisations need to make their minds up whether or not they want that to happen or not," he said.
"I think the organisations can be left under no doubt whatsoever that what the Government and what the HSE wants to see is strict compliance with public sector pay policy.
"They've got a number of different routes they can pursue to ensure that."