HIQA has found that 11 centres for people with disabilities did not have evidence of Garda vetting for all staff.
The centres in the north-west of the country also had incomplete staff records, such as full employment histories.
Inspectors said that this meant that they felt they were not assured that residents were appropriately safeguarded against risk.
One centre - Ox View Community Houses in Sligo - was informed in November its registration would be cancelled due to ongoing failures.
HIQA found that the HSE's proposed response had not been fully implemented during an inspection in December.
It said this was having a negative impact on residents, but since the inspection the HSE had taken additional actions to improve its quality of service.