Extracts from the unpublished sections of the Madonna House report were revealed in the last programme in RTE's States of Fear series last night.
They show that management of the Dublin home was aware of complaints of sexual abuse from many children over an eight-year period but failed to stop it.
Children complained to staff, who in turn complained to the management of the home, according to the report.
Madonna House was owned by the Irish Sisters of Charity, who closed it in 1993 in the wake of a child-abuse investigation.
It had been used extensively by the Eastern Health Board as a place of safety for children at risk of neglect or abuse.
The report on the inquiry into Madonna House was not published until 1996 and then only partially by the Fine Gael-Labour-Democratic Left coalition. A member of that government claimed last night that the report had never come to cabinet and was dealt with at the Department of Health.
Last night's programme also detailed abuses at St Joseph's Residential Centre in Kilkenny. David Murray, a childcare worker, and others abused numerous children at the centre in the 1970s. The programme claimed management at the centre knew abuse was going on in the late 1970s.
It also claimed information was given to Sister Stanislaus Kennedy, then of Kilkenny social services, in the 1970s that children were being physically abused at the centre.
Sister Stanislaus, now director of Focus Ireland, told The Irish Times early today that a worker at the home had told her of his concerns about physical abuse. She had advised him to complain to management and, as a result, the person involved in the physical abuse had been dismissed.
She was "totally unaware" that any sexual abuse was going on. The programme aimed to show that institutional abuse did not simply stop when big facilities such as Letterfrack, Co Galway, and Artane, Dublin, were closed in the late 1960s.
The programme alleged that abuse investigations have been held at more than 20 childcare residential centres in the 90s.
The States of Fear series created an unexpected public reaction. That extreme abuses occurred was already well known, but the programme featured victims talking of their experiences and created a wave of revulsion.
Package of measures on childhood sex abuse announced yesterday by the Taoiseach, Mr Ahern, following the screening of the RTE documentary series State of Fear:
Commission to inquire into childhood abuse
Professional counselling service for victims of abuse - estimated cost £4 million a year.
Legal changes relating to taking of cases involving abuse.
Publication of proposals relating to mandatory reporting of abuse.
Creation of a register of child sex offenders.
Implementation of range of other measures - unspecified - to protect children at risk.