The HSE was reacting to the fallout from the top-up payments to senior employees in charities.
It said all charities had until the Feb 21 deadline to put forward a business case stating why they think their top executives should be paid more than the public sector threshold, or face the funding cut.
The five charities which have yet to comply are: St James’ Hospital, St James’ University Hospital, St John of Gods and the Brothers of Charity’s South and South East organisations.
The HSE said since last December it had undertaken a “comprehensive engagement process with all full or part-funded Section 38 agencies (charities) to address compliance with public pay policy”.
Yesterday it provided an update on its progress to the Public Accounts Committee having asked the charities to submit information by last Monday.
Up until then it said 10 agencies are deemed compliant with pay policy and a total of 88 business cases had been received from another 27 agencies.
Five, however, were still to detail a response and are currently deemed as non-compliant, running the risk of funding cuts.
The organisations deemed to be compliant include Incorporated Orthopaedic Hospital, Clontarf; KARE, Cork University Dental School and Hospital; St John’s Hospital, Limerick, Mercy University Hospital, Cork and St Vincent’s Hospital, Fairview.
Those who are have lodged business cases include the Brothers of Charity in Clare and Galway, Rotunda Hospital, Beaumont Hospital and the Children’s University Hospital at Temple Street.