The HSE is denying it was forced to slow its clampdown on top-up payments.
It was previously reported that some State-funded health agencies claimed they were "legally obliged" to continue making those payments to eight senior executives.
The HSE said that that while some non-salary allowances can be allowed, no decision has yet been made.
"Some of those organisations asked us for legal indemnification in the event that it may end up in court and we have said that there are no circumstances where we'll grant such indemnification," said Barry O'Brien is the HSE's national director for human resources.
"We employ, and have a pay policy for 97,500 people.
"We have a very small number, and we are methodically, best practice, based on best governance, ensuring that all of those people get into compliance."