'Culture of silence'
Drawing on statements from thousands of former students and officials, the report accused successive generations of priests and nuns of beating, starving and raping children in state-run institutions.
The report said there was a "culture of silence" among church leaders who turned a blind eye to the abuse.
The largest-ever probe into Irish religious orders found abusers could "operate undetected for long periods at the core of institutions" while victims were sometimes blamed as having been corrupted and "punished severely".
It said girls, although suffering much less sexual abuse than boys, experienced frequent assaults and humiliation.
"In some schools a high level of ritualised beating was routine ... Girls were struck with implements designed to maximize pain and were struck on all parts of the body," the report said.
"Personal and family denigration was widespread."
'Sorry and ashamed'
Cardinal Sean Brady, the head of the Catholic church in Ireland, said: "I am profoundly sorry and deeply ashamed that children suffered in such awful ways in these institutions."
Batt O'Keeffe, Ireland's education minister, said: "Child abuse is an abhorrent, inexcusable act whenever and wherever it occurs.
"As a responsible and caring society, we must fully face up to the fact that wrong was done and we must learn from the mistakes of the past."
The commission interviewed 1,090 men and women who were housed in 216 institutions including children's homes, hospitals and schools.
Many of the children were sent into church care because of school truancy, petty crime or because they were the offspring of unmarried mothers.
'Deceived and cheated'
The report was met with mixed responses from victims of abuse in Catholic institutions.
John Kelly, of the Survivors of Child Abuse group, said survivors felt "deceived and cheated".
"There is nothing by way of justice in any means significant in this report, nothing," he said.
But Christine Buckley, one of the main campaigners on behalf of abuse victims, said the report would "hopefully close another chapter in the hard lives of survivors".
"I earnestly hope that the recommendations made in this report will safeguard children in care at present and in the future," she said.
Revelations of abuse have eroded the Catholic Church's moral authority in Ireland.
The inquiry was announced in 1999 by Bertie Ahern, the then prime minister, after he apologised to victims following revelations made in a series of television documentaries.