'Disturbing issues' have come to light inside St Patrick's Institution, the detention centre for 18 to 21-year-old offenders.
They have been uncovered by the Director of Prisons Judge Michael Reilly just as a plan to take younger teenagers out of the jail over the next two years gets under way.
Judge Reilly expresses his concerns in his annual report but does not expand on the nature of the issues.
He began an investigation into St Pat's in 2011 with unannounced visits at nights and weekends.
"Since commencing this investigation certain 'disturbing issues' have come to light. This investigation is far reaching and time consuming," he says.
"I will submit my report to the Minister in due course."
The institution has long been regarded as a "finishing school for criminals" and as far back as 1985 the renowned TK Whitaker called for its closure.
Children's Minister Frances Fitzgerald recently announced that younger teenage offenders are to be taken out of St Pat's within two years in an attempt to stop them ending up in Mountjoy Prison next door.
She has received €50m in funding to build a 60 room centre at Obserstown in Lusk which already accommodates young offenders.
St Pat's houses 44 offenders aged 16 and 17 -- a situation described by Children's Ombudsman Emily Logan as a serious breach of international human rights.
The Director of Prisons has had to delay key elements of his Prisons' report for varying reasons.
The two-year Strategic Plan announced recently by the Irish Prison Service has prompted the inspector to defer a planned assessment of the current prison system and suggestions for the future.
The Inspector also planned to comment on the health care of prisoners from a physical and mental point of view.
But this has also been deferred until after the publication of a report by the Commission of Investigation into the death of Gary Douch, who was murdered in a holding cell at Mountjoy on August 1, 2006.
Other elements of a report on all aspects of prison life will be contained in a report to be issued in August.
Judge Reilly is also investigating circumstances surrounding the the death of Shane Rogers, who was found hanged on December 20, 2011 in a holding cell at Cloverhill courthouse after admitting shooting dead Crossmaglen GAA star James Hughes in Dundalk following a row over his ex-girlfriend.