MINISTER for Health James Reilly has warned St Vincent's Hospital that it is "heading for serious trouble" if it does not co-operate with a HSE audit of pay and allowances.
The HSE is currently auditing voluntary hospitals and disability organisations in receipt of public money.
The investigation is to discover exactly how much they have been paying senior staff in private allowances.
However, St Vincent's Hospital said it was not appropriate to provide the details, as public funds were not involved in the payments.
Mr Reilly said it was very unfortunate that the hospital had refused to provide the details to the HSE.
"I think that it's very unfortunate. I think it is very clear that people need to be in compliance and part of compliance was cooperation," Mr Reilly said on RTE's Morning Ireland.
"If St Vincent's are not co-operating, they are heading for serious trouble in my view and serious consequences for that hospital."
The Dáil Public Accounts Committee has said it is "not good enough" that St Vincent's Hospital has refused to provide the details.
The PAC is due to receive a report today from the HSE and the Department of Health on whether the hospitals and agencies are complying with government guidelines.
The move comes after the controversy over so-called top-up payments to senior executives at the Central Remedial Clinic which resulted in the board resigning last week.