LONDON - For more than a half century, thousands of children in church-run orphanages and reform schools in Ireland were severely abused by priests and nuns, a government commission said yesterday in the first official accounting of a scandal that has wrenched the deeply Roman Catholic nation.

The 2,600-page report, which capped a nine-year investigation, said rape and sexual abuse were "endemic" in boys' institutions funded by the state but run by the church. "A climate of fear, created by pervasive, excessive and arbitrary punishment, permeated most of the institutions and all those run for boys," it said.

In general, the commission found, the severe physical and sexual abuse that occurred in boys' schools was absent in girls' schools. It said "emotional abuse," including humiliation and denigration, was common in institutions for girls.

More than 300 people who now live abroad, including in the United States, returned to Ireland to testify at 166 hearings on what happened to them. In all, more than 1,000 people, most now in their 50s or older, described rapes, molestations, floggings, scaldings, and other abuse.

From the 1930s to the 1990s, Ireland educated tens of thousands of orphans and other children ages 5 to 16 - including those with disabilities or born to unwed mothers or with histories of petty crime - in 200 crowded, 19th-century institutional homes.

The commission was set up by the Irish government and headed by High Court Justice Sean Ryan.

"I am profoundly sorry and deeply ashamed," Cardinal Sean Brady said after the report was released yesterday in Dublin. "Children deserved better and especially from those caring for them in the name of Jesus Christ."

The commission said documents found at the Vatican showed that religious orders knew of numerous abuse complaints but covered them up.

The Christian Brothers ran many of the boys homes, and more allegations were made against it than against all other male religious orders combined.

The order successfully sued the commission in 2004 to keep accused members unnamed, noting that many of the brothers were dead and could not defend themselves.

In the end, no priest or nun was named in the report - a fact many of the victims groups decried, because the findings will not aid those pursuing criminal prosecutions.

"It's deeply flawed, incomplete, a whitewash," John Kelly, coordinator of the Survivors of Child Abuse, an Irish victims' group, told reporters in Dublin.

John Walsh, who described himself as a victim of abuse, told Irish reporters that he was "very angry, very bitter" that no priests were named.

Some church defenders suggested that victims may have exaggerated their claims. But many Irish commentators portrayed the report as a devastating indictment of both the church and the state.

The report strongly criticized the Irish Education Department for lack of oversight, describing how a state inspector could be responsible for as many as 50 schools and would typically announce visits in advance.

At Dublin's Artane Industrial School for 800 boys, sexual abuse was "chronic" and physical punishment was "excessive and pervasive and, because of its arbitrary nature, led to a climate of fear among the boys," the panel found.

It said in some girls' schools "a high level of ritualized beating was routine."

In part because of a deferential attitude to the clergy, Education Department officials often failed to investigate claims of abuse, the commission noted.

In the worst cases, children who complained were "blamed and seen as corrupted by the sexual activity and punished severely," it said.

Ireland's myriad religious orders, much like their mother church, have been devastated by 15 years of scandals involving cover-ups of abusers. "Most of these orders will literally die out in Ireland within the next generation or so," said Michael Kelly, editor of the Irish Catholic newspaper in Dublin.

A government panel has paid 12,000 survivors an average of $90,000 each - on condition they surrender their right to sue the church or state. About 2,000 claims are pending. Irish Catholic leaders cut a controversial deal with the government in 2001 that capped the church's contribution at $175 million - a fraction of the final cost.