New Hiqa reports show there needs to be better hand hygiene practices at three regional hospitals.
The body also said it is not confident about infection prevention management at Portiuncula Hospital, Ballinasloe.
At the end of last year there was an extensive outbreak of Clostridium difficile infection at Portiuncula Hospital.
The infection affects the bowel and causes diarrhoea.
Hiqa said that measures to prevent another outbreak need to be introduced and they are not assured the incident is being effectively managed.
They also reported concerns about the hospital's preparedness for an outbreak of Legionella.
Unannounced visits were also made to Sligo University Hospital and Galway University Hospital.
In both cases they found the hospitals were largely up to scratch, but some further hygiene management services were needed.