Two of Dublin's busiest hospitals were found to not be in compliance with infection prevention and control practices, HIQA has found.
The healthcare inspection body visited five hospitals between January and March, including Beaumont and Mater Misericordiae University.
Only one hospital, Louth County, was found to be in compliance.
Beaumont, Mater, Wexford General and University Hospital Waterford were all found to have risks.
Beaumont Hospital had its compliance with oversight of performance across clinical areas but found that patients were still being admitted to a CPE outbreak ward.
HIQA said: "Beaumont Hospital had experienced an ongoing outbreak of CPE on one ward since August 2018.
"Although a number of mitigating measures had been implemented on the outbreak ward, new cases of CPE continued to be identified over the following six months.
"This inspection identified that the hospital was continuing to admit patients to a CPE outbreak ward which had been closed to admissions; this was contrary to advice from the infection prevention and control team.
"It was also of significant concern to HIQA, who escalated concerns to the hospital related to this finding following the inspection. The ward was closed to admissions on the week beginning 18 February 2019."
Despite the concerns surrounding the presence of CPE in the hospital earlier this year, HIQA noted strong leadership, management and oversight arrangements, standardised processes with up-to-date standard operating procedures and a culture of audit, feedback and quality improvement.
A Beaumont Hospital spokesman told Dublin Live: "Beaumont Hospital welcomes the support provided by HIQA. The ward already closed to admissions on day of HIQA inspection thereby enabling a full ward decant and subsequent ward refurbishment of all areas. The ward has reopened. There is no CPE positive patient on ward."
When visiting the Mater Hospital, the inspection body found that two outbreaks of CPE had been controlled by the hospital in critical care areas.
A programme for infection prevention and control was in process of being re-established after key positions were left vacant.
HIQA said: "HIQA acknowledges the outbreak control committee had had successfully controlled two outbreaks of CPE transmission in critical care areas.
"Nothwithstanding this positive finding, inspectors also found that the local infection prevention and control risk register was not being managed and escalated in line with national guidance.
"While the hospital had defined leadership and management arrangements in place for decontamination service provision, inspectors found that governing and oversight structures to support the service were not clearly defined.
"Additionally, decontamination-related risks had not been effectively managed. There was a need to embed a culture of continuous audit, feedback and quality improvement cycles in relation to decontamination and reprocessing procedures across the hospital."
