Asylum seekers lodged just 47 complaints with the Reception and Integration Agency about the Direct Provision system last year.
The figure, provided by the Department of Justice, comes amid confirmation that the DP system now has exceeded its capacity and has had to access emergency bed spaces.
Nick Henderson, the CEO of the Irish Refugee Council, said there were "several issues" with the relatively low number of complaints, including the likelihood that some asylum seekers would be wary of making a complaint about the centre in which they live amid an expectation that little, if anything, would change.
He said some asylum seekers may not be aware of the complaints mechanism and would also be wary of lodging a complaint with RIA, while they may also feel the scope of any possible complaint would be quite limited.
He said a complaint regarding transfer between different centres may not be entertained at all.
"Also people may be wary of complaining to the body which is providing accommodation," he said. "They need to probably see examples of the complaints mechanism working before they themselves pursue it."
Figures provided to RTE showed there are currently 6,355 people in Direct Provision, above the contracted capacity on January 20 of 6,156.
RIA has had to access emergency bed spaces in hotels since last September due to insufficient capacity in the system, while two properties earmarked to house asylum seekers have been targeted in arson attacks in recent months.
The Irish Refugee Council (IRC) said any works that could be carried out within Direct Provision centres have also been stalled or rolled back because essentially all rooms in the system were now in use.
Mr Henderson said the capacity issue was not a surprise because of delays in making decisions about status, an increase in the number of people seeking asylum and particularly because of the effect of the overall housing crisis.
The Irish Refugee Council said there were 700 people currently in the DP system who had already secured their status to stay in Ireland, but who could not move on because of a lack of available accommodation and an associated lack of means to secure that accommodation.
Mr Henderson argued that the Government would have to secure more accommodation space to get past the crisis and that another potential difficulty faced by some people who have been granted asylum here was "racism or discrimination, direct or indirect" when they seek access to private rented accommodation.
The IRC has said the full welfare allowance should be granted on refugee status, as well as an extension of the Housing Assistance Payment scheme.