The current system of international protection accommodation is not adequately resourced to meet demand according to the Health Information and Quality Authority (HIQA).
HIQA has published a one-year overview report on its monitoring and inspection of the centres, formally known as direct provision.
The watchdog said there is "considerable room for improvement" around governance, management, risk management, safeguarding and protection.
HIQA met more than 860 adults and 300 children and young people over the course of inspections last year.
A total of 41% of residents living in the accommodation centres had received refugee status or had valid permission to remain in Ireland, but continued to live in accommodation centres due to a lack of alternatives.
The report found that overall, a lack of resources has had "a notable impact" on the quality of accommodation and services that are being provided to some people seeking protection in Ireland.
Bronagh Gibson, HIQA Head of Programme for Monitoring International Protection Accommodation Service Centres, told RTÉ's News at One that sixty inspections of 51 centres were carried out and that some were inspected more than once.
It was was found there are "some very good providers...they meet the national standards, so they comply with what's required of them," but "there is overcrowding in [accommodation] centres".
HIQA did not find any centre that was "operating outside of its contracted numbers... but very cramped environments," she added.
She gave examples of six unrelated adults sharing a bedroom, and a family of eight sharing a very small mobile home with two newborn babies.
She said this "lack of alternative accommodation" was the "most commonly-cited reason" for overcrowding, and that some 1,100 adults and children HIQA have been "directly spoken" to for not moving out of IPAS accommodation.
She said the report also "highlights the need for a review of the current centres to make sure that they are providing effectively what they should provide to the people that they are designed provide for."
A total of 74% of service providers had limited or no systems in place to identify or monitor risk in their centres and 37% of centres inspected by HIQA did not have policies and procedures in place to protect residents from experiencing harm.
Urgent action was required last year when the watchdog discovered that 35% of staff across the centres were not appropriately vetted by An Garda Síochána, however, HIQA said it is "currently assured" that relevant staff members have now been appropriately vetted.
The report shows that when it comes to the safety and protection of asylum seekers from risk, challenges remain.
A total of 56% of centres inspected did not have effective governance and management arrangements in place and had poor, or no, reporting systems and these need to be strengthened to ensure that high-quality, safe services are being provided, according to the report.
The regulator identified seven key areas to promote the delivery of safe and effective accommodation centres including building capacity within the international protection accommodation system along with an ongoing assessment of the capacity of need.
The Department of Children, Equality, Disability, Integration and Youth has welcomed the publication of HIQA's overview report.
It said that where any centre has areas of partial or non-compliance identified following an inspection, a bespoke Compliance Plan is agreed.
There are specific and time-bound measures taken in order to ensure full compliance with the National Standards and HIQA.
It said IPAS has noted that "ongoing improvement" is seen through this process.
The Garda National Vetting Bureau prioritises vetting of staff for family accommodation centres, where children are accommodated, it added.
It said that under the National Vetting Bureau (Children and Vulnerable Persons) Acts 2012 to 2016, all staff of international protection accommodation centres who work with children are required to be garda vetted prior to commencing employment.
