Nearly half of the teenagers who were held in Trinity House juvenile detention centre ended up in adult prison within six months of their release from the young offenders' facility, according to the report.
The only data available on children after their release from centres is for Trinity House, where 57 boys aged under 16 were released in 2002. After six months, 24 of those were in jail, three is residential care with a health board, two were homeless and one had returned to Trinity House. The whereabouts of two were unknown.
According to the report, there have been no independent inspections of Trinity House and Oberstown boys and girls centres, all on the same campus in Lusk. This is despite an independent review in 2002 which recommended an independent inspection system be in place by March 2003.
The review also urged the establishment of a single board of management with a chief executive officer for all five residential schools under the Department's control.
The comptroller also found that there were no performance measures for the schools, which also include St Joseph's in Ferryhouse, Co Tipperary, and Finglas Child and Adolescent Centre.
The report highlighted difficulties at Finglas, where child numbers were cut in half because the centre was in "acute crisis".
According to the report, key legislation on the operation of the centres could not be implemented because new detention facilities for 16 and 17-year-olds were not available, and there was no sign from the Department of Justice when it intended to provide these.
In response, the Department of Education said the establishment of a new single board of management was delayed because of a potential overlap and conflict with other provisions.