The HSE says it has contacted gardaí after allegations €50,000 has vanished from the bank accounts of vulnerable patients.
The HSE confirmed to the Irish Independent that it had discovered "what may be irregularities in service user accounts in one of the community group homes".
It was reported over the weekend that the money was missing from a number of residents' accounts at St Joseph's Intellectual Disability Service at St Ita's Hospital in Portrane, Dublin.
An employee at the centre of the investigation was reported to be a trusted staff member who assisted residents withdrawing money from cash machines.
A source told the 'Sunday Mirror' that the staff member has been suspended from duty while the investigation is carried out. It centres on allegations of withdrawals from six accounts over an 18-month period.
"The HSE has confirmed that it has discovered what may be irregularities in service user accounts in one of its Community Group Homes," a spokeswoman said.
"Staff have spoken with the relevant service users and their families to advise them of the suspected irregularities.
"The HSE deeply regrets any upset which this alleged incident might cause but has reassured the service users and their families that if any discrepancies are discovered in any of their personal accounts, they will be fully reimbursed.
"The HSE has contacted An Garda Síochána and a Garda investigation is proceeding. The HSE has also begun its own investigation."
The intellectual disability service at the hospital offers services for older people with intellectual disability, home support services, assistance for those with challenging behaviour, residential care and day care and respite beds for adults.
When the Irish Independent contacted the hospital, a spokesperson redirected queries to the HSE for comment.
Fine Gael TD for Fingal Alan Farrell issued a statement on the hospital two days before the reports of missing money which highlighted other concerns.
Mr Farrell said he was anxious to hear of the "poor condition" of the hospital for service users after a Mental Health Commission inspection report.
"The HSE has stated it now plans to work with the service users and their families . . . in order to find them a place to live which is more suitable to their needs and which will provide quality of life," he said.
"While I do not believe it to be acceptable that service users have been accommodated in premises which are of poor condition, I am relieved that action is being taken to provide them with more appropriate accommodation."