The reports have been published by the Health Information and Quality Authority.
Our Lady's Children's Hospital Crumlin in Dublin received a largely positive report after its inspection.
However, after an unannounced inspection of South Tipperary General, HIQA inspectors warned that the risk of hospital infections was not being managed.
Emergency department curtain rails were heavily soiled with black dust.
Grit and pieces of waste paper were found on the floor of a maternity ward storage room for baby feeds.
Sligo Regional Hospital and the South Infirmary Victoria Hospital in Cork were criticised for poor hand hygiene practices.
During an unannounced inspection at the Rotunda Maternity Hospital in Dublin, inspectors found unsecured chemical storage, clinical waste and sterile equipment.
But there is praise for Our Lady's Children's Hospital, where the paediatric intensive care unit and patient equipment were found to be exceptionally clean.