An inspection of four hospitals around the country has found just one was in full compliance with guidelines on screening for the superbug CPE.
HIQA's infection prevention and control inspections took place in hospitals during June and July.
Inspections were carried out at Our Lady's Children's Hospital, Crumlin, St Columcille's Hospital, Loughlinstown, Croom Orthopaedic Hospital, Co Limerick and Mallow General Hospital, Co Cork.
HIQA monitors infection prevention and control in hospitals against the national standards for the prevention and control of healthcare-associated infections in acute healthcare services.
These inspections were conducted by HIQA following the declaration of a national public health emergency plan to address Carbapenemase-Producing Enterobacteriales (CPE) last October.
CPE is a very resistant type of bacteria that can cause serious infections.
HIQA's inspections focused on how hospitals are implementing the national standards, with a particular examination of how patients are being protected against the CPE threat.
HIQA found only one of the four hospitals inspected - Croom Orthopaedic Hospital - were in full compliance with the HSE guideline.
It says: "Given that the threat associated with CPE has been declared a national public health emergency, HIQA escalated concerns to hospital management in three hospitals and the HSE to seek assurances around how each hospital might ensure compliance with the HSE's own guidelines."
Each hospital then outlined how it intends to address this issue.