HIQA inspections at hospitals in Cork and Limerick have raised concerns about hand hygiene, cleanliness, infections and overcrowding.
The findings were made during visits to University Hospital Limerick and Cork University Hospital - including the maternity hospital - in November 2014 and January this year.
HIQA wants a review of the management and monitoring of hand hygiene practices at both University Hospital Limerick and Cork University Hospital, after initial inspections found they were not up to standard.
The authority is warning both of the need to improve 'considerably' to hit national hand hygiene targets set by the Health Service Executive (HSE).
The first inspections in November also identified risks in relation to the cleanliness of patient equipment and the environment in some wards at the hospitals, but there were improvements by the January re-inspections.
In the University Hospital Limerick report, HIQA highlighted the on-going need to tackle multi-drug resistant infections - but said a significant amount of work had been done.
HIQA also found that more needs to be done to improve hand hygiene at the hospital, epecially among non-nursing staff.
It says it has contacted the HSE at senior level to advise them of the extra cost to the hospital in tackling the issue.
It wants the hospital to be given all necessary supports to ensure the risk is managed as well as possible on a system-wide basis.
Concerns were also raised about overcrowding in Limerick, with reports from staff that this was a near-permanent situation due to overcrowding throughout the hospital.
HIQA says both hospitals must now revise and amend their quality improvement plans, and publish them on their websites in six weeks.
The inspections on both hospitals were unannounced, HIQA says.