Minister for Justice Alan Shatter has said the culture outlined in the report on St Patrick's Institution has been brought to an end.
He said a substantial programme of reform has been put in place and the vast majority of it has already been implemented.
He said the remaining 40% of staff will have completed retraining next month.
Children's Ombudsman Emily Logan said she was patronised and made fun of when she reported on conditions at St Patrick's last year.
Ms Logan said senior officials at the Department of Justice had an attitude of indifference towards the young offenders and had no respect for them because they had broken the law.
"Last year I was, I suppose, patronised somewhat and made fun of, if you like, and made to believe that I was a bit naive in thinking that what the young people were saying is true," she said.
"So effectively if you have young people who were in conflict with the law, we're not expected to believe what they are saying."
She said the findings were reminiscent of the revelations in the Ryan Report into abuse at State and church-run institutions.
Ms Logan, who visited St Patrick's last week, said the young people there were definitely still fearful of making a complaint.
She said there was a new and open approach from the new director of the prison services and felt confident about the commitment of the new governor at the institution to improve conditions.
Mr Shatter said there is new management and better oversight at the institution and young adults will no longer be housed there from 2014.
He said investigations are under way into particular officers and a new complaints procedure will be in place from November.
Panel to investigate historical complaints
A new panel of independent investigators will also be asked to address historical complaints.
The Irish Prison Service said a number of staff members at the institution are being investigated following the publication of the Inspector of Prisons' report.
The report on the detention centre found that a minority of prison officers and staff bully, intimidate and provoke inmates, including children.
Irish Penal Reform Trust Executive Director Liam Herrick said it was not known whether the officers accused of bullying are still working at St Patrick's.
Speaking on RTÉ's Morning Ireland, Mr Herrick said the report showed certain groups of young men being treated in a scandalous fashion.
He said while a new governor has been appointed, it is not known if the individuals concerned have been identified.
The Prison Officers' Association said the report raises many important issues, "including the urgent need to provide training for prison officers in dealing with young offenders".
In 1985, the Whitaker Report recommended St Patrick's Institution be closed.
Now, 25 years and several reports later, the latest report details the mistreatment and degradation of children there, with some being forcibly restrained and their clothes being ripped and cut off them.
While the majority of the 198 staff deal with the inmates in a professional, courteous and proper manner, the report is highly critical of a minority who bully, intimidate and provoke retaliation, which results in disciplinary measures being taken against the prisoners.
The IPS said internal disciplinary inquiries are under way into the behaviour of a small number of staff and these could result in some cases in dismissal.
Issues 'had been raised before' - Chaplain
Head of the Prison Chaplaincy Team, Fr Ciaran Enright has said that issues raised in the report had been raised before.
Speaking on RTÉ's News at One, Fr Enright said that chaplains and many other bodies, including European bodies, had voiced concerns about the treatment of children and young men in St Patrick's.
Fr Enright said that he hopes that this report will be listened to and will be acted upon.
"What's different and what's new is the detail and the facts that are outlined in such a systematic and frightening way, a really horrifying way to see those facts laid out, and those truths laid out. But they have been spoken before, time and time again and I suppose as a group of Chaplains, we're hoping now that maybe this is the report that will be listened to."
He added that with posters urging voters to vote "yes for children" in relation to the upcoming referendum, that this must include a "yes for the children and young men" in State care in St Patrick's Institution.
"It's still continues that we have young men locked up behind their doors some for 23 hours a day, many for 17 hours a day, and we kind of ask ourselves, is this what we mean looking at posters all over the country where we're saying "yes for children" in the upcoming referendum.
“Is this what yes for children means because if we're saying yes for children, the children and young adults in St Patrick's Institution must be part of that yes."
Elsewhere, Clare Daly TD has criticised the delay in making the report public, saying the report was submitted to Minister Shatter many months ago.
She said that three-and-a-half-months is "a long time in prisons terms, in fact it could be a whole sentence for some young person".