It is not the memories of the kickings and lashings with a leather strap that make Tom Hayes pause and choke and break down. Nor is it the incessant bullying, the slave labour or the sexual abuse he suffered after dark in the dormitory. The memory that turns the 63-year-old former soldier's voice small with terror is one vivid image from his eight years in Glin industrial school, Limerick. "The first time I saw someone brought back to the school having absconded was one of the most frightening things I've ever witnessed," he says. "His head was shaved as punishment and then he took a really serious beating by two Christian Brothers. I've never forgotten it."

The trauma for Hayes and others has been stirred up again this week by the fourth major report in the past decade investigating the abuse of children by Ireland's Catholic clergy and teachers. A day before the government report made new revelations of the collusion of the Irish police and archbishops in covering up decades of sexual and physical torture, the Christian Brothers, the Catholic lay order at the heart of some of the most disturbing abuses, offered reparations of £145m in cash and land, to be handed over to independent trusts.

The revelations have all but destroyed a dying institution, in Ireland at least, where there are barely 250 Brothers left with an average age of 74. Last year they ceded control of 96 schools to a charitable trust, marking the end of two centuries of the Brothers educating boys in Ireland. The order may be diminished but its legacy still looms large over thousands of lives – and the development of Ireland. As Jim Beresford, who was confined to Dublin's notorious Artane school as a boy, puts it: "Ireland made the Christian Brothers and then they made Ireland."

It is difficult to overstate the Brothers' influence on Ireland. The boys it educated became the men who created the republic, its Dáil and its literature. Of 15 men executed for leading the Irish uprising of 1916, seven were Brothers' alumni. Ireland "owes more than it probably will ever realise to the Christian Brothers," said Eamon de Valera, the independence leader who later became taoiseach and president after attending a Brothers' school. Gerry Adams, Martin McGuinness, Charles Haughey and Bertie Ahern were Brothers' alumni. Irish writers educated by the Brothers include Roddy Doyle, Colm Tóibín and Ronan Bennett. Even James Joyce, a Jesuit, spent a short time at a Brothers' school. The order followed the Irish diaspora to Britain, Canada and Australia and John Birt, Brendan Barber and Tony Booth, father of Cherie, are alumni of the Brothers' St Mary's College, Crosby.

An Irish merchant, Edmund Rice, founded the Christian Brothers in Waterford in 1802. Dáire Keogh, an Irish historian, says one of their "foundation myths" was that they were established to teach poor boys when in fact they were created to provide a Catholic education, which had been outlawed in Ireland. The Brothers rejected the non-denominational schools system established by the British in 1831 and ran their schools independently. This, Keogh says, was fundamental in forging their uncompromising curriculum, which included an explicitly Catholic and patriotic emphasis, which shaped Ireland's national identity.

Rice banned the physical punishment of children – a radical idea at the time. So how did his principles become so perverted? Strapped for cash, Brothers were paid by results so they pushed their boys, hard, to get scholarships to stay in secondary education. Outside the state system, their schools were poorly supervised, allowing abuse to flourish. Even when they returned to the state system after Irish independence in the 1920s, they remained relatively unsupervised by state or church. And Brothers' alumni formed much of the new civil service, giving the group powerful political influence. "The lack of supervision is part of the whole problem," says Keogh.

Ireland only introduced free secondary education in 1968. Before then, the Brothers' cheap schools opened up secondary education to thousands of families who could not otherwise afford it. "That's where they were really influential," says Keogh. According to Barry Coldrey, an Australian-based Brother turned historian who has uncovered evidence of widespread abuse, the Brothers proved "very successful in shoving young men up the social scale". Physical abuse was "tolerated so long as the Brothers delivered educational success" says Coldrey, who recalls a parent saying to him when he was teaching more than 30 years ago: "Do anything you like to him to get him through his exams."

Coldrey argues there is evidence the Brothers' leadership knew of sexual abuse in its schools as early as the 1920s. And the order's real achilles heel, he says, was its Dickensian industrial schools. Hayes was taken to Glin industrial school aged eight in 1954. Woken at 7am for mass, breakfast would be two slices of bread; lunch was potatoes and a bit of meat; supper was two more slices of bread. In the morning he had lessons; then he would work in the school tailors or farm for up to five hours. After tea, he played in the yard before being confined to his dormitory of 40 boys by 7pm. "Night time could be frightening," he says. "My very first experience of sexual abuse was when I woke up to find somebody with his hand under my blanket. He was lying under my bed."

The Brothers ruled through monitors: boys of 16 who kept order by bullying everyone in their dormitories. Hayes was not sexually abused by the Brothers, although he was regularly beaten. But when he complained about being sexually abused by other boys, he was simply beaten up by his monitor.

Why did the Christian Brothers' schools perpetuate such abuse? Hayes thinks "they lost sight of their own founder's expectations" when they ambitiously "moved into educating the elite of Ireland", setting up schools that weren't just aimed at the poor. Meanwhile, their industrial schools became just that: industries, feeding the Brothers' other, more glamorous projects, including Irish sports. "We were free labour. They made a great deal of money from it," says Hayes. "We were just cannon fodder for them."

Attempts to contextualise the abuse can make historians appear to be apologists. While 35,000 children went to Brothers' schools and other church-run institutions in the decades after the 1930s, it is not known how many were victims of abuse. There are plenty of alumni who praise their education. A former pupil of St Mary's College, Crosby, in the 1980s, recalls regular beatings and believes the Brothers' regime was certainly more violent than other public schools. But he says he would still send his children to a Brothers' school if he thought it offered the best education.

In Ireland, the Brothers' industrial schools were vast and anachronistic. "Artane was a residential school for 900 boys," says Keogh. "These were Victorian institutions that died out in Britain in the 19th century. They survived in Ireland until the 1970s and that is the problem." Keogh argues that the Brothers gave Ireland the schools it demanded. "That's what the Irish wanted: containing people who didn't fit through the cookie cutter – the poor, problem children, single mothers. It was the architecture of containment."

Now a semi-retired teacher who lives in Huddersfield, Jim Beresford was forcibly removed from his family by the Irish courts at 13 and says he was locked away for two years in what he still calls "prison": Artane. When he escaped, the gardaí pursued him – a practice the latest report reveals was commonplace. "Never in my worst nightmares had I ever dreamed such a place could exist," he says. "When I arrived, I was shocked by the wretchedness of the prisoners. I had seen the newsreel footage of the liberation of Belsen and that's what it looked like. Many of them had their heads shaved off as punishment and were behind bars."

Beresford argues that the Brothers' brutality is rooted in the teachings of Rice, its founder, who modelled himself on Ignatius and was "heavily into self-mortification". Self-flagellation was then routine in the Catholic church. "Pain and suffering was good for the soul. If suffering is good, it's a short step to saying, 'why not inflict it?'" Brothers joined the order as teenagers; they were taught to whip themselves as punishment for their sexual urges and discipline their pupils for sexual indiscretions. In an institution that demanded celibacy and yet was riven with "sexualised violence", some Brothers became sexual sadists, argues Beresford. The impact on Ireland has been profound. "The politicians, the businessmen, the priests, all went to Christian Brothers schools and absorbed the diet of violence, religious intolerance and sadomasochism," he says. Beresford wrote in the Irish Times: "To a large extent [the Christian Brothers'] mindset is Ireland's mindset. Their sadomasochism is an unacknowledged part of Irish male identity."

Keogh disagrees. "I don't think there was anything in the theology which made abuse OK. The problems were in the structures," he says. Self-flagellation was a universal idea in the Catholic tradition until the early part of the last century. "To make the jump between that and abusing children is oversimplistic and a misunderstanding of the theology," he argues. "The whole Christian Brother phenomenon was of its time. They mirrored society rather than moulded it."

The Brothers' influence faded with the introduction of universal secondary education and the increasing secularisation of Ireland. Then came revelations of abuse. The Christian Brothers apologised in 1998 but victims were dismayed at its half-heartedness. Earlier this year – after Brothers' legal action successfully preserved their individual anonymity – the Ryan report confirmed that sexual abuse was "endemic" in boys' institutions, chiefly those run by the Brothers. Many victims, however, remain sceptical that they will ever see any of the proffered reparations money and are convinced that the authorities continue to conceal the scale of the suffering.

Its Irish victims are also appalled that the order continues to thrive outside Ireland. These days, the Brothers' leader is Indian and the order is active in India, 13 African countries and across north and South America, although with more of an emphasis on social work. "They are one of Ireland's major exports," says Beresford. "This isn't just an Irish problem. These guys went all over the world and carried their evil methods with them."

In Ireland, the Brothers run retreat centres, help prisoner rehabilitation and, according to Brother Edmund Garvey, a member of its Dublin-based European leadership team, have spent the past six years critically examining their religious life. Part of the problem, says Garvey, was their "dualism" that separated human life from spiritual life; living in small centres, some of the order are now considering whether to permit non-celibacy. He says the order is very willing to meet victims and has done so since the Ryan report. "If anybody wants to meet with us we are totally open, willing and ready," he says.

Asked about the positive contribution of the Brothers, Garvey points out: "There is a huge number of Brothers who never sexually abused or physically abused people in an unwarranted way. The abusers are not the total story."

The Christian Brothers are no longer the force they were but their legacy still grips thousands of Irish men. Like many victims, Tom Hayes fled Ireland. He found refuge in the British army, where he served for 42 years. "Many of us still suffer from some kind of post-traumatic stress disorder. Many of us are loners. Many of us are workaholics or alcoholics or take drugs. Fear and insecurity has plagued me throughout my life."

For much of our long conversation, Hayes is polite and almost meek towards his abusers. He says he still feels angry though, because he believes the Christian Brothers are still in denial and refuse to engage with victims. "They seem to be totally disinterested in hearing from us. No matter how well we have done or how sane we are, they still regard us with contempt." It sounds almost like he is still seeking their approval. "We were children. We didn't do anything wrong. We were used and abused and yet even to this day somehow we have a sense of guilt that we can't for the life of us get rid of."

Additional reporting by Ian Sansom

How the church's secret came to light



June 1995

October 2005 The Ferns report is published detailing extensive child abuse and cover-up in the south-east of Ireland. Among those investigated was Father Sean Fortune. He later committed suicide rather than face his victims.

2005 The Murphy Commission is established 10 years after complaints by more than 400 people against 43 priests in the Dublin diocese. Costing more than €3m (£2.7m), the inquiry takes four years. Former victims who played a key role in exposing the scandal included Andrew Madden, who was abused as an altar boy.

May 2009 The Ryan report focuses on church-run industrial schools, orphanages and the Magdalene laundries. The main religious orders criticised include the Irish Christian Brothers and several orders of nuns including the Sisters of Mercy. The report vindicates claims by hundreds of former inmates and orphans that they were subject to regimes of physical brutality and sexual exploitation. Among those who led the campaign to reveal the truth was Thomas "Anto" Clarke. He spoke to the Observer in 1998 and his testimony prompted other victims to come forward and establish the campaign group Irish Survivors of Child Abuse, which fought for an Ireland-wide inquiry.

November 2009 A report on the abuse of children by clergy in Dublin from the early 1970s to date is published. It accuses the church hierarchy in Dublin of covering up reports of abuses, and says Ireland's police force colluded. Victims' campaigners are now demanding that Pope Benedict (pictured) personally apologises. Two priests have been suspended. Henry McDonald