The introduction of regulation for residential centres for people with disabilities has brought about a positive cultural change in the sector, according to HIQA.
The Health Information and Quality Authority said that two years ago, initial inspections found that residents in many large congregated settings were not being adequately protected or kept safe.
But it adds that inspections steadily led to improvements in their standard of care.
HIQA's inaugural Overview Report of Disability Inspections says initial inspections in 2014 uncovered a lack of understanding on the part of service providers on how to meet regulations and standards.
Inspectors found residents living in many large congregated settings who were not being adequately protected. Longstanding institutionalised care practices were impacting adversely on their quality of life.
However, the review praises the steady improvements in care it says regulation prompted last year when HIQA inspected 561 of the 937 designated residential centres for adults - and mixed centres for adults and children - with disabilities.
However, the watchdog warns that the positive trend was not universal and that it had to commit significant resources to inspecting centres where residents' safety had been breached. And it took enforcement action in a number of them.
Formal court enforcement procedures were used in respect of four centres last year resulting in one being taken over by the Health Service Executive and restrictive conditions being placed on the registration of the three others.
The Chief Inspector of Social Services and Director of Regulation at HIQA has said standards of care at residential centres for people with disabilities are improving.
Speaking on RTÉ's News at One, Mary Dunnion said that HIQA will act "without fear or favour" where concerns about safety or quality of services exist.
Today, the Seanad passed a proposal to extend the automatic registration period of all centres for a further two years.
HIQA has said that this will allow it to continue to focus on the highest-risk facilities it has identified, and is continuing to identify, in its comprehensive series of inspections.
In the Dáil, Sinn Féin's Carol Nolan requested an independent root-and-branch inquiry to all care homes for people with disabilities.
Tánaiste Frances Fitzgerald said everyone was aware of the poor standards in some residential care homes for people with disabilities and she commended HIQA for the work it has done revealing poor standards in some residential services.
Ms Fitzgerald said €300m has been dedicated for residential services to reach proper standards.
The minister also said top-ups should be returned and she pointed out that the Ministers for Public Expenditure and Health are analysing the situation to ensure action is taken so money due to the State is recouped.
Ms Nolan said there was a plan to register 1,000 of the centres by this year, and this has not happened.
Therefore, she said, she would not be singing the praises of HIQA.