For decades, retired Cardinal Roger Mahony and other high ranking members of the Roman Catholic Archdiocese of Los Angeles made secret efforts to shield child molesting priests. Their aim was to keep their parishioners in the dark and control the damage to the church, church personnel files have revealed.

According to the Daily Mail, previously confidential records filed in a lawsuit against the archdiocese disclose how the church handled abuse allegations for decades. They also reveal that a top Mahony aide criticized his superiors for covering up all the allegations of abuse, rather than protecting children and alerting the authorities.

Notes signed by Mahony demonstrate that he was disturbed about abuse cases being reported to him and that he sent accused priests for treatment, but psychological reports that he received on some priests mention the possibility of many other victims, and there is no indication he or other church leaders investigated them.

'This is all intolerable and unacceptable to me,' Mahony reportedly wrote in 1991 on a file concerning Reverend Lynn Caffoe, a priest suspected of locking boys in his room where he videotaped their crotches. He also ran up a $100 phone sex bill while with a boy.

Caffoe was sent for therapy and removed from ministry, but Mahony didn't actually move to defrock him until 2004, a full decade after the archdiocese lost track of him.

'He is a fugitive from justice,' Mahony wrote to the Vatican's Cardinal Joseph Ratzinger, who is now Pope Benedict XVI. 'A check of the Social Security index discloses no report of his demise, so presumably he is alive somewhere.'

Caffoe died in 2009, six years after a newspaper reporter found him working at a homeless mission two blocks from a Salinas elementary school.

Mahony released a statement on Monday apologizing for his mistakes and saying he had been 'naïve' about the lasting impacts of abuse. Reporters were told he was out of town and unable to make further statements.

Mahony has reportedly met with 90 abuse victims privately and keeps an index card with each victim's name in his private chapel, where he prays for them daily. The card also includes the names of the molesting priests 'lest I forget that real priests created this appalling harm.'

Mahony inherited a list of offending priests from his predecessor when he took over in 1985, J. Michael Hennigan, an archdiocese attorney, told the Daily Mail. Hennigan added that priests were sent out of state for psychological treatment because therapists were not required to report their child abuse offenses to law enforcement as they were in California, he said.

The files reveal that one priest victimized the children of illegal immigrants and then threatened to have them all deported if they told authorities.

When Reverend Nicholas Aguilar Rivera molested in LA, the files allege, church officials waited two days to call police, allowing him to flee to Mexico. At least 26 children told police they had been abused during his ten months in Los Angeles. The now-defrocked priest is believed to live in Mexico and remains a fugitive from law enforcement.

The personnel files of 13 other clerics show a similar pattern of denial and cover-up, said attorney Anthony De Marco, who represents one 35-year-old plaintiff.

The growing tide of abuse and the church's habitual secrecy in response to it saw one memo to Mahony suggest sending a cleric to a therapist who also is an attorney, in the hope that any incriminating evidence would be protected from authorities by lawyer-client privilege.

In another instance, archdiocese officials paid a secret salary to a priest who had been exiled to the Philippines after he and six other clerics were accused of having sex with a teen and impregnating her.

The newly published files offer a startling glimpse at the 30,000 pages still to be made public as part of a record-setting $660 million abuse settlement.

The archdiocese agreed to give the files to the more than 500 victims of priest abuse in 2007, but a lawyer for about 30 of the accused priests fought to keep records sealed. A judge recently ordered the church to release them without blacking out the names of church personnel.

The files demonstrate how church leaders moved 'problem' priests from parish to parish for decades, covering up each report of abuse and failing to contact law enforcement.

Mahony, who retired in 2011 after twenty six years at the helm of a 4.3-million person archdiocese, has come in for particular criticism for his handling of the case of the Reverend Michael Baker, sentenced to prison in 2007 for molestation, two decades after he confessed his abuse to Mahony.

Mahony sent Baker for psychological treatment in 1986 after the priest told him that he had molested two brothers over seven years. Baker returned to ministry the next year with a doctor's recommendation that he be defrocked immediately if he spent any time with minors. But despite several documented instances of being alone with boys, Baker wasn't removed from ministry until 2000.

Church officials also reportedly discussed announcing Baker's abuse in churches where he had worked, but Mahony rejected the idea.

'We could open up another firestorm — and it takes us years to recover from those,' Mahony wrote in an October 6, 2000, memo. 'Is there no alternative to public announcements at all the Masses in 15 parishes??? Wow — that really scares the daylights out of me!!'

The aide, Monsignor Peter Garcia Richard Loomis, noted his dismay over how higher ups were handling the matter when he retired in 2001 as vicar for clergy, the top church official who handled priestly discipline. In a memo to his successor, Loomis said Baker's attorney disclosed the priest had at least 10 other victims.

'We've stepped back 20 years and are being driven by the need to cover-up and to keep the presbyteriate & public happily ignorant rather than the need to protect children,' Loomis wrote.

'The only other option is to sit and wait until another victim comes forward. Then someone else will end up owning the archdiocese of Los Angeles. The liability issues involved aside, I think that course of complete (in)action would be immoral and unethical.'

But Mahony preferred targeted warnings at schools and youth groups to a blanket warning read at Masses, Hennigan said. Parish announcements were only made two years later.

Baker was paroled in 2011 and is alleged to have molested 20 children in his 26-year career. The newly released files show that Mahony worked tirelessly to keep molester priests out of state to avoid criminal and civil consequences.

Cardinal Rogery Mahony celebrates a Mass at the Cathedral of Our Lady of the Angels in downtown Los Angeles in this May 2006AP