Beaumont Hospital in Dublin was continuing to admit patients to a ward which was closed due to an outbreak of the CPE superbug.
That is one of the findings of a report by the health watchdog, which carried out an inspection in February of this year.
HIQA carried out infection prevention and control inspections at five different hospitals in the first quarter of this year.
They are Wexford General Hospital, University Hospital Waterford, Louth County Hospital and Dublin hospitals Beaumont and the Mater.
Inspectors found only the Louth hospital was in compliance with HSE guidelines on screening patients for CPE.
They raised significant concerns with the management of Beaumont Hospital, which has been dealing with an outbreak of the bug in one ward since August 2018.
It was found that at the time patients were still being admitted into the ward despite it being closed.
The report also stated University Hospital Waterford needs to address issues around decontamination systems and to place regular auditing procedures into practice.
Wexford General Hospital management were told to address equipment and hospital hand hygiene compliance but had met appropriate standards in other areas.
Overall, HIQA found recurring challenges to effectively prevent and control the CPE outbreak, such as ageing hospital infrastructure, a lack of isolation facilities and high occupancy rates.