Ombudsman for Children Emily Logan has asked the Oireachtas committee on Health and Children to look into the issues at the Oberstown detention centre in north county Dublin.
Speaking on This Week on RTÉ Radio One, Emily Logan said she believes the move to the site by the middle of next year is under threat.
The Oberstown centre in Lusk has been identified by Government as the primary detention centre for young people under-18 but in recent months three judges have raised issues over places available for youth detention.
Circuit Court Judge Mary Ellen Ring said a lack of youth detention places was making what she called a "mockery" of the court.
Ms Logan said there are serious issues surrounding resources and staff and that deadlines could be missed.
She has written to the Oireachtas Committee on Health and Children to ask it to call in those who are accountable for the project.
Ms Logan said she would like to see the board of management explain the problems that exist at the site. She added that the young people who go there have no one to represent them.
The Irish Reform Penal Trust has also expressed concern. Spokesperson Liam Herrick said that progress must be made immediately because St. Patrick's institution may be closed earlier than envisaged.
Spokesperson for IMPACT, the union that represents workers at Oberstown, Catherine Keogh said management presented a new rostering proposal last Friday. She said this would be addressed with urgency.
She said resources are an issue at Oberstown but the union was intent on meeting its deadlines, to ensure the transition to Oberstown for all young people, by the middle of 2014.
In a statement to RTÉ, the Minister for Children and Youth Affairs Frances Fitzgerald said "work is ongoing to ensure that extra bed spaces will be available in the coming weeks."
She said "The Irish Youth Justice Service has developed proposals to make these beds available through a reorganisation of where bed spaces are used on the campus.
"The issues of resources, training and staffing are common challenges across the public sector at present and are the subject of ongoing discussion between management and staff on the campus, and the Irish Youth Justice Service."