More than half of hospitals and health agencies are in breach of public sector pay rules, it has emerged.
In 12 cases, the organisation was compliant with the rules that prohibit unauthorised payments - or so-called top-ups - to senior staff.
Health Minister James Reilly said eight institutions have yet to respond to the HSE's request for information.
"The HSE's approach involves a robust process of verification and, as necessary, clarification of the position in each Section 38 organisation," Dr Reilly said.
"Until such time as the situation in each organisation has been fully verified, none of these organisations can be deemed fully compliant."
Dr Reilly insisted the Government is determined to ensure that public pay policy is "respected and complied with".
He received the update from the HSE today on steps being taken to ensure compliance with public sector pay policy.
The executive had written to the 44 hospitals and health agencies in September asking whether their pay arrangements to staff comply.
Under the rules, bodies that receive public funding must not supplement approved pay rates with either money from the state or non-Exchequer sources, such as charitable donations.
The policy states that any organisation wishing to make a business case for the payment of unapproved allowances can do so and it will be considered by the HSE.
Yesterday, Rhona Mahony, the top doctor at the National Maternity Hospital at Holles Street, said she had been vilified and faced unwarranted criticism over her earnings in the row over top-up pay.
She insisted her wages are strictly in line with public sector rules and that any additional money she earns is from her private practice.
Dr Mahony said she earned an additional 45,000 euro in private fees last year and accused the media of labelling it a "top-up".
She said the rest of her salary was strictly in line with her contract at Holles Street and complied exactly with wider health service rules.
The payments controversy erupted after health watchdog Hiqa discovered last year that a senior manager at Tallaght Hospital was paid an additional 150,000 euro in payments since 2005.
The health minister ordered the HSE to conduct an audit of pay at the 44 hospitals and agencies.
They had until Tuesday night to return all the information requested.
Taoiseach Enda Kenny yesterday warned that those who fail to respond will be hauled before the Government to explain themselves.