The confidential records filed in a lawsuit against the archdiocese disclose how the church handled abuse allegations for decades and also reveal dissent from a top Mahony aide who criticized his superiors for covering up allegations of abuse rather than protecting children.

Notes inked by Mahony demonstrate he was disturbed about abuse and sent problem priests for treatment, but there also were lengthy delays or oversights in some cases. Mahony received psychological reports on some priests that mentioned the possibility of many other victims, for example, but there is no indication that he or other church leaders investigated further.

“This is all intolerable and unacceptable to me,” Mahony wrote in 1991 on a file of the Rev. Lynn Caffoe, a priest suspected of locking boys in his room, videotaping their crotches and running up a $100 phone sex bill while with a boy. Caffoe was sent for therapy and removed from ministry, but Mahony didn’t move to defrock him until 2004, a 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 was out of town but issued a statement Monday apologizing for his mistakes and saying he had been “naive” about the lasting impacts of abuse. He has since 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, he said. The card also includes the name of the molesting priest “lest I forget that real priests created this appalling harm.”

“It remains my daily and fervent prayer that God’s grace will flood the heart and soul of each victim, and that their life journey continues forward with ever greater healing,” Mahony wrote. “I am sorry.”

The apology stands in contrast to letters Mahony was writing to accused priests more than two decades ago.

In 1987, he wrote to the Rev. Michael Wempe — who would ultimately admit to abusing 13 boys — while the priest was undergoing in-patient therapy at a New Mexico treatment center.

“Each of you there at Jemez Springs is very much in my prayers and I call you to mind each day during my celebration of the Eucharist,” Mahony wrote to the priest, adding that he supported him in the experience.

The church’s sex abuse policy was evolving and Mahony inherited some of the worst cases from his predecessor when he took over in 1985, J. Michael Hennigan, an archdiocese attorney, said in a separate series of emails. Priests were sent out of state for psychological treatment because they revealed more when their therapists were not required to report child abuse to law enforcement, as they were in California, he said.

At the time, clergy were not mandated sex abuse reporters and the church let the victims’ families decide whether to contact police, he added.

In at least one case, a priest victimized the children of illegal immigrants and threatened to have them deported if they told, the files show.

The files are attached to a motion seeking punitive damages in a case involving a Mexican priest sent to Los Angeles in 1987 after he was brutally beaten in his parish south of Mexico City.

When parents complained the Rev. Nicholas Aguilar Rivera molested in LA, church officials told the priest but waited two days to call police — allowing him to flee to Mexico, court papers allege. At least 26 children told police they were abused during his 10 months in Los Angeles. The now-defrocked priest is believed to be in Mexico and remains a fugitive.

The personnel files of 13 other clerics were attached to the motion to show a cover-up pattern, said attorney Anthony De Marco, who represents the 35-year-old plaintiff. In one instance, a memo to Mahony discusses sending a cleric to a therapist who also is an attorney so any incriminating evidence is protected from authorities by lawyer-client privilege. In another instance, archdiocese officials paid a secret salary to a priest exiled to the Philippines after he and six other clerics were accused of having sex with a teen and impregnating her.

The exhibits offer a glimpse at some 30,000 pages to be made public as part of a record-setting $660 million settlement. The archdiocese agreed to give the files to more than 500 victims of priest abuse in 2007, but a lawyer for about 30 of the priests fought to keep records sealed. A judge recently ordered the church to release them without blacking out the names of church higher-ups after The Associated Press and the Los Angeles Times intervened.

They echo similar releases from other dioceses nationwide that have shown how church leaders for decades shuffled problem priests from parish to parish, covered up reports of abuse and didn’t contact law enforcement. Top church officials in Missouri and Pennsylvania were criminally convicted last year for their roles in covering up abuse, more than a decade after the clergy sex abuse scandal began to unfold in Boston.

Mahony, who retired in 2011 after 26 years at the helm of the 4.3-million person archdiocese, has been particularly hounded by the case of the Rev. Michael Baker, who was sentenced to prison in 2007 for molestation — two decades after the priest confessed his abuse to Mahony.

Mahony noted the “extremely grave and serious situation” when he sent Baker for psychological treatment after the priest told him in 1986 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. Despite several documented instances of being alone with boys, the priest wasn’t removed from ministry until 2000. Around the same time, the church learned he was conducting baptisms without permission.

Church officials 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 Oct. 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, Msgr. Richard Loomis, noted his dismay over 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.”

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

Baker, who was paroled in 2011, is alleged to have molested 20 children in his 26-year career. He could not be reached for comment.

The files also show Mahony corresponded with abusive priests while they underwent treatment out of state and worked to keep them out of California to avoid criminal and civil trouble.

One case involved the Msgr. Peter Garcia, a molester whom Mahony’s predecessor sent for treatment in New Mexico. Mahony kept Garcia there after a lawyer warned in 1986 that the archdiocese could face “severe civil liability” if he returned and reoffended. Garcia had admitted raping an 11-year-old boy and later told a psychologist he molested 15 to 17 young boys.

“If Monsignor Garcia were to reappear here within the archdiocese, we might very well have some type of legal action filed in both the criminal and civil sectors,” Mahony wrote to the director of Garcia’s New Mexico treatment program.

Mahony then sent Garcia to another treatment center, but Garcia returned to LA in 1988 after being removed from ministry. He then contacted a victim’s mother and asked to spend time with her younger son, according to a letter in the file.

Mahony moved to defrock him in 1989, and Garcia died a decade later.