The mental health charity St John of God has said rental income was used to pay €2m in secret top-ups to its senior management.
The revelation comes as charities have been urged to publish all transactions on their websites.
Under-fire charity St John of God said "rental income" was used to give secret "buyouts" to senior management.
The payments were made after strict pay caps were imposed in 2013 on charities who are largely State-funded.
The charity will now be subject to a HSE probe following the revelations.
The €2m was split between 14 senior managers.
However, no record of the payments was made in any publicly-filed document.
The HSE has said it was unaware of any such payments, but will now launch an investigation.
A spokesman for St John of God said the payments did not come from State funding (of which it receives about €125m of its €150m budget).Services were also not affected, he added.
However, Ivan Cooper (inset) of The Wheel - a charities support group - said that charities must consider all money public money.
"Trust is the most important asset that a charity has. All funds under the control of the charity should be regarded as public funds, irrespective of where it comes from," he said.