At a mass in the Vatican on 6 October 1996 to celebrate the beatification of Edmund Rice, Cardinal Cahal Daly delivered a homily eulogising the Christian Brothers, the order Rice founded. He thanked the brothers for educating generations of Irish children, specifically mentioning children from poor families. Addressing a congregation swelled by 22 leading churchmen from Ireland as well as the Minister for Defence, a junior minister, several front bench spokesmen and the deputy leader of Fianna Fáil, the cardinal added: "I wish to say that the bad image sometimes given to the brothers in some sectors of the press and media is totally unjustified, unfair and unjust." None of the church or state dignitaries raised a dissenting voice.

Three years later, the Commission to Inquire into Child Abuse was established. Its five-volume final report, published last Wednesday after nine years of hearing witness testimonies, shows who exactly was telling the truth about the Christian Brothers, and who was not. The main reason it took the commission almost a decade to complete its work was because the Christian Brothers did their damnedest to stop the truth coming out.

Despite issuing an apology as long ago as 1998 to "anyone who suffered ill-treatment while in our care", they resisted disclosure at every turn. That was their strategy. When members of the order faced trials in the criminal courts for sexually abusing children, the brothers sought judicial reviews, frequently with success, to have the trials abandoned on the grounds that too much time had elapsed since the alleged offences. When survivors of abuse turned to the civil courts in search of compensatory justice, the brothers bare-facedly denied the allegations, causing victims more distress. On Newstalk last Thursday morning, after the publication of the abuse commission's report, Brother Edmund Garvey urged anyone who had suffered to go to the courts with their cases. The hypocrisy of his order's position was breathtaking.

The commission did not conceal its disgust with the brothers who were, the report states, "co-operative in terms of production of documents but defensive in the way it responded to complaints". One example of how the religious teaching order continued to deny, deny, deny is contained in an act of grotesque abuse by a brother on a child in Artane industrial school where, the report states: "The safety of children was not a priority at any time during the relevant period." A witness to the commission told how he was ordered to lick faeces off the shoe of a brother, who thrashed him when he had done so. The man identified as the perpetrator by the witness verified the account and admitted his guilt. Despite this, his order continued to insist the incident never happened.

"Complaints were not handled properly and the steps taken by the congregation to avoid scandal and publicity protected perpetrators of abuse," the report observes. To judge by the brothers' attitude to the commission itself, little has changed.

Though unsuccessful in their High Court attempt to restrict the commission's remit and to stop it inquiring into the extent of physical and sexual abuse, the Christian Brothers ultimately succeeded in preventing it from naming abusers, whether dead or alive, convicted of crimes or not.

Judge Ryan's report offers an insight into the commission's dealings with the brothers. It says they made statements they knew to be "incorrect or misleading", omitted relevant facts and denied that a brother was ever in an institution where a witness "got a name even slightly wrong". It was because of their bull-headed resistance to the commission's investigation that an immunity deal was deemed necessary. They fought disclosure every step of the way. When, in August 2007, the archbishop of Dublin, Diarmuid Martin, released the confidential 1961 report by former Artane chaplain, Fr Henry Moore, which had been commissioned by his predecessor John Charles McQuaid in 1962, the Christian Brothers made it known they were "shocked and dismayed" by Martin's decision.

By the time Moore came to write his report on the dire conditions in Artane, the case of Mickey Flanagan had been raised in Dáil Eireann. At 13 in 1953, he was punished for being involved in a schoolyard brawl. A brother grabbed the child's arm and twisted it repeatedly like the hand of a clock until it broke in three places. His mother was not allowed to see him for eight days. His father called for a public inquiry. Nothing happened.

Donal Dunne's 40 years of abuse

The most horrifying exposure of the Christian Brothers' complicity in covering up crimes against children – and thereby facilitating them – was in the case of Donal Dunne. His 40-year career as a child sex-abusing teacher began as a Christian Brother. He was granted voluntary dispensation from his vows after three incidents of abuse, and progressed thereafter through six different schools where "he terrorised and sexually abused children in his classroom", according to the report. "At various times during his career, parents attempted to challenge his behaviour but he was persistently protected by diocesan and school authorities and moved from school to school. Complaints to the Department of Education were ignored."

In February 1999, the year the commission was set up, Dunne was jailed for a further two years on 16 counts of indecent assault on seven boys between 1965 and 1969. Had his superiors in the Christian Brothers taken action to stop him, instead of letting parish priests write glowing job references to secure him a school principalship, countless other children could have been saved from him. This was brought starkly home in the mid-1990s when Dunne was again convicted, this time for abusing a 12-year-old boy in 1995, when the former brother, who began abusing at the age of 21, was aged 74.

The commission describes the Christian Brothers' apology to victims as "guarded, conditional and unclear". Why, therefore, should anybody accept in good faith the words of contrition issued by the order since the report's publication on Wednesday? They have known about the abusers in their midst for decades. As far as their knowledge is concerned, little changed between the period before the report was published and the period since.

In recent times, the Christian Brothers' 96 schools in Ireland, with 35,000 students and 2,700 teachers, have been transferred to the auspices of the Edmund Rice Schools Trust but the order cannot wash its hands of the thousands of children whose care was entrusted to them in the industrial schools system.

As renewed controversy rages about the state's over-generous indemnity deal with religious orders, there must be survivors of those horrors who are aghast that the public's concentration has so quickly switched to the cost to the taxpayer rather than the imperative of calling to account the people in positions of responsibility who consistently covered up for child abusers.

Ireland has an abysmal track record in tackling the crime of sheltering criminals. Only two cases involving the charge of accessory-after-the-fact appear in the Law Reports. A new criminal offence of reckless endangerment of children was created by the Criminal Justice Act 2006 as a result of the Ferns Inquiry, but nobody has yet been charged with the crime. It came into effect on 1 August 2006. Under the law, a person with authority or control over a child, or an abuser, can be found guilty if it's proven that they intentionally or recklessly endangered the child by putting them in a situation where there was a risk or by failing to take reasonable steps to prevent that risk.

While church and state colluded in concealing abuse throughout the industrial schools system, the Christian Brothers' intransigence towards the state's commission of inquiry has compounded the order's transgressions against humanity. Their conduct gives a very hollow ring to Blessed Edmund Rice's ideal: "Catholic and Celtic, to God and Ireland true".