"This report makes it clear that great wrong and hurt were caused to some of the most vulnerable children in our society," he said.
"It documents a shameful catalogue of cruelty: neglect, physical, sexual and emotional abuse, perpetrated against children."
The five-volume study concluded that church officials encouraged ritual beatings and consistently shielded their orders' paedophiles from arrest amid a "culture of self-serving secrecy".
It also found that government inspectors failed to stop the chronic beatings, rapes and humiliation.
The findings will not be used for criminal prosecutions - in part because the Christian Brothers successfully sued the commission in 2004 to keep the identities of all of its members, dead or alive, unnamed in the report.
Victims campaigners protested at being excluded from the news conference
No real names, whether of victims or perpetrators, appear in the final document.
Police were called to the commission's news conference amid angry scenes as victims were prevented from attending.
One of the many victims, John Walsh of Irish Survivors of Child Abuse, said the absence of prosecutions had left him feeling "cheated and deceived".
"I would have never opened my wounds if I'd known this was going to be the end result," he said.
"It has devastated me and will devastate most victims because there are no criminal proceedings and no accountability whatsoever."
More allegations were made against the Christian Brothers than the other male orders combined.
The report found child safety was not a priority for the Christian Brothers who ran the institutions, the order was defensive in its response to complaints and failed to accept any congregational responsibility for abuse.
The report said that girls supervised by orders of nuns, chiefly the Sisters of Mercy, suffered much less sexual abuse but frequent assaults and humiliation designed to make them feel worthless.
The leader of the Roman Catholic Church in England and Wales, the Most Reverend Vincent Nichols, said those who perpetrated violence and abuse should be held to account, "no matter how long ago it happened".
The reformatory and industrial schools depended on rigid control by means of severe corporal punishment and the fear of such punishment
"Every time there is a single incident of abuse in the Catholic Church, it is a scandal. I would be very worried if it wasn't a scandal... I hope these things don't happen again, but I hope they're never a matter of indifference," he said.
The commission said overwhelming, consistent testimony from still-traumatized men and women, now in their 50s to 80s, had demonstrated beyond a doubt that the entire system treated children more like prison inmates and slaves than people with legal rights and human potential.
"The reformatory and industrial schools depended on rigid control by means of severe corporal punishment and the fear of such punishment," it said.
"The harshness of the regime was inculcated into the culture of the schools by successive generations of brothers, priests and nuns.
"It was systemic and not the result of individual breaches by persons who operated outside lawful and acceptable boundaries.
"Excesses of punishment generated the fear that the school authorities believed to be essential for the maintenance of order."
The report proposed 21 ways the government could recognise past wrongs, including building a permanent memorial, providing counselling and education to victims, and improving Ireland's current child protection services.
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