Only two religious orders audited by child safety watchdogs have demonstrated good compliance with rules to protect youngsters from abusers.
Following reviews last autumn, the National Board for Safeguarding Children in the Catholic Church in Ireland (NSBCCCI) warned seven congregations have considerable work to do on the issue.
The two orders praised by the review team were the Congregation of the Sacred Hearts, an order with 18 priests working and living in London, Dublin and in the Cavan-Monaghan area, and the Dominican Sisters, based in Dublin, Galway, Wicklow and in the North, working largely in education.
Teresa Devlin, chief executive of the NBSCCCI, warned that much work was needed for seven orders to fall into line with the official child protection standards.
"In relation to the large reviews, I'm disappointed that, for the majority of Orders, the whole area of safeguarding is only being bedded down in the last couple of years," she said.
"Of the nine only two orders have demonstrated good compliance with the standards, and have demonstrated their commitment to putting in place good safeguards for children as well as prompt responses to allegations of abuse. For the other seven there is considerable work to be done."
The board found poor record management in many cases making an assessment of child protection practice difficult.
Opportunities to safeguard children were missed, known abusers were allowed to remain in ministry in 1990s.
The board - the Catholic Church's own watchdog in Ireland - found management plans relating to accused priests and nuns have improved significantly over time but it warned there is still room for improvement, in terms of clarity of roles, review of restrictions, and sharing of information.
It noted that support for complainants is good in many cases with evidence of pastoral support, outreach and direct contact with survivors of abuse.
The board warned of variable delays in reporting allegations to the civil authorities up until 2009 but it also said some practices did not improve until 2013.
"A series of recommendations have been made within each report and the board expects that these will be acted upon," Ms Devlin said.
The board has requested the orders to make progress reports on the recommendations in nine months.
In the case of the Franciscan Friars, the watchdog points out that there were three "prolific" abusers within their ranks, although allegations had been levelled against 28 friars since 1975.
A significant number of the sexual abuse allegations relate to two friars, both of whom were convicted and served prison sentences.
One remains under supervision within the Order while the other left in 2003.
The watchdog said the Franciscans either delayed or failed to notify state authorities about the abuse and also delayed taking action under the Order's own canon law.
Furthermore, the Order had poor records of contact with victims and of monitoring friars under supervision.
It was concerned that the Order seemed to put more importance on legal processes rather than the pastoral support of victims in some cases.
"It is the opinion of the reviewers that civil settlements provide financial compensation but do not address other needs including counselling, care and support for the survivor," the report states.
"A more caring pastoral response is required and this is being reflected in the current Minister Provincial's willingness to reach out to survivors publicly in recent months."
In a statement, the Order's Minister Provincial, Hugh McKenna, said the report describes "the stark reality of abuse perpetrated" by Irish Franciscans over a 45-year period and also highlights the Order's "failure" to deal with the abuse.
"We regret that there were significant missed opportunities, as highlighted in the report, in terms of protecting other children from abusive behaviour," he said.
"As Provincial of the Irish Franciscans, I apologise unreservedly to each and every survivor for the pain and harm inflicted on those who suffered abuse while under our care.
"I apologise for the breach of trust, and the suffering victims and their families endured.
"I also know that no apology can ever be sufficient, and acknowledge with deep shame and sadness that the Franciscan Order failed you."
The report notes a change in safeguarding practices since 2009, which it says was further strengthened under Fr McKenna since his appointment in July 2011.