Beatings and humiliation by nuns and priests were common at institutions that held up to 30,000 children, Ryan report states

Rape and sexual molestation were "endemic" in Irish Catholic church-run industrial schools and orphanages, a report revealed today.

The nine-year investigation found that Catholic priests and nuns for decades terrorised thousands of boys and girls in the Irish Republic, while government inspectors failed to stop the chronic beatings, rape and humiliation.

The high court judge Sean Ryan today unveiled the 2,600-page final report of Ireland's commission into child abuse, which drew on testimony from thousands of former inmates and officials from more than 250 church-run institutions. Police were called to the news conference amid angry scenes as victims were prevented from attending.

More than 30,000 children deemed to be petty thieves, truants or from dysfunctional families – a category that often included unmarried mothers – were sent to Ireland's austere network of industrial schools, reformatories, orphanages and hostels from the 1930s until the last facilities shut in the 1990s.

The findings prompted the new Archbishop of Westminster, the Most Rev Vincent Nichols, to say that it took "courage" for those clergy involved in child sex abuse to confront their actions. In an interview to be broadcast tonight on ITV News at Ten, he said: "I think of those in religious orders and some of the clergy in Dublin who have to face these facts from their past which instinctively and quite naturally they'd rather not look at. That takes courage, and also we shouldn't forget that this account today will also overshadow all of the good that they also did."

The Irish Survivors of Child Abuse (Isoca), an organisation set up to help victims, condemned the newly appointed head of the Catholic Church in England and Wales for his remarks.

"Rubbish is too kind of word for what the archbishop has said. I believe I have heard this kind of twaddle uttered by politicians in Ireland like Bertie Ahern, the former prime minister. It is the verbiage of un-reason and it leaves me cold. What the Archbishop really has to do is take a long hard look at the character and nature of the people he is talking about and ask himself if they are capable of being good," said Patrick Walsh.

The report found that molestation and rape were "endemic" in boys' facilities, chiefly run by the Christian Brothers order, and supervisors pursued policies that increased the danger. Girls supervised by orders of nuns, chiefly the Sisters of Mercy, suffered much less sexual abuse but instead endured frequent assaults and humiliation designed to make them feel worthless.

"In some schools a high level of ritualised beating was routine ... Girls were struck with implements designed to maximise pain and were struck on all parts of the body," the report said. "Personal and family denigration was widespread."

The report concluded that when confronted with evidence of sex abuse, religious authorities responded by transferring offenders to another location, where in many instances they were free to abuse again.

"There was evidence that such men took up teaching positions sometimes within days of receiving dispensations because of serious allegations or admissions of sexual abuse," the report said. "The safety of children in general was not a consideration."

The Catholic church had been steeling itself for the report, which was repeatedly delayed by church lawsuits, missing documentation and alleged government obstruction.

The Christian Brothers delayed the investigation for more than a year with a lawsuit that successfully defended their members' right to anonymity in all references in the report, even in cases in which individual Christian Brothers had been convicted of sexual and physical attacks on children.

The church had already been under fire over the sexual misbehaviour of several priests in various Irish parishes. The commission's experts have sought to produce a comprehensive portrait of sexual, physical and emotional damage inflicted on the child victims. The thousands of survivors said they had no safe way to tell their stories until the investigation began because much of Irish Catholic society regarded them as liars.

Isoca today said it was now up to the Vatican to investigate its religious orders in the republic.

John Kelly, the Isoca co-ordinator in Dublin, said: "Now that the Ryan [Laffoy] commission is finished, we call upon ... Pope Benedict XVI to convene a special consistory court to fully investigate the activities of the Catholic religious orders in Ireland.

"Amongst other things, such a court could establish the whereabouts of Irish state assets that were misappropriated over many years by the religious orders and make restitution to the Irish state exchequer."

During the commission's investigations, oral evidence was collected from more than 1,000 people, mainly aged from their 50s to 70s.

Several hundred travelled back to Ireland from the US and Australia to describe their childhood of terror and intimidation.

One victim, John Walsh, of Isoca, called the report a hatchet job that left open wounds gaping. "The little comfort we have is the knowledge that it vindicated the victims who were raped and sexually abused," he said.

"I'm very angry, very bitter, and feel cheated and deceived. I would have never opened my wounds if I'd known this was going to be the end result. It has devastated me and will devastate most victims because there is no criminal proceedings and no accountability whatsoever."

The commission's original judge, Mary Laffoy, resigned from her post in 2003 over claims that the Irish department of education – which was in charge of inspecting the orphanages and industrial schools – was refusing to hand over documents to her.