Hospitals were hindered by poor infrastructure, limited bed capacity and staffing levels as they tried to respond to the covid pandemic.
Last year, HIQA says none of the 10 hospitals it inspected was fully compliant with cleanliness and safety standards aimed at minimising the risk of infection spreading.
The report says they did not have enough single en-suite rooms along with an insufficient number of showering and toilet facilities.
A hospital in the Shannonside region was found to be only partially compliant in the aspect of minimising health risks during the pandemic.
The health watchdog has published a report on how hospitals coped during Covid, including the Midlands regional Hospital in Mullingar.
It was found to be compliant in two areas, with three substantial compliances also recorded.
The only partial compliance was around if "healthcare was provided in a clean and safe physical environment that minimises the risk of transmitting a healthcare-associated infection."
Overall, four hospitals were not providing healthcare in a clean and safe environment that minimised the risk of infection spreading.
HIQA says Mayo and Tallaght University Hospitals as well as Naas and Wexford General Hospitals were not compliant with the standard during its inspections last year.