Initially, he said last month that he had no recollection of the priest speaking to him about abusing boys. Mahony acknowledged that he would probably remember such a meeting if it had occurred.
On Tuesday, Mahony confirmed in his letter to archdiocese priests that Baker had confessed to him.
"Sometime in late 1986, Baker disclosed to me that he had problems in the past of acting out sexually with two minors," Mahony wrote.
Priests and parents at the three parishes where Baker had served until 1986 said the archdiocese failed to inform them about any reported sexual abuse by Baker.
In explaining his response, Mahony told the priests: "Baker was sent to a treatment center for evaluation and recommendation for his future. Following treatment, it was decided that he could do specialized priestly ministry not related to children and youth. He was subsequently given various ministries, such as special outreach to our retired priests."
Mahony also required Baker to undergo continued counseling and banned him from having one-on-one contact with minors.
The cardinal blamed Baker for not being honest during his twice-a-month counseling sessions.
"Baker's truthfulness was questionable," Mahony said in an interview, adding that "we never found any evidence of cooperation. He deceived his therapists, everybody."
In addition, Baker continued to have frequent access to children over the next 14 years while he was assigned to nine different parishes. Six of the churches where Baker worked had elementary schools adjacent to the rectory: St. Thomas the Apostle in Los Angeles, St. Elizabeth in Van Nuys, St. Linus in Norwalk, St. Mary in Palmdale, St. Lucy in Long Beach and St. Columbkille in South-Central Los Angeles.
Records and interviews also show that Baker was sent to at least three parishes to fill in for pastors who had either retired or been transferred, leaving no superior to monitor his day-to-day activities.
"Mainly, I was a pinch-hitter to keep things running smoothly," Baker said of his relief duties.
In his message to priests, Mahony said the archdiocese received no reports of sexual abuse involving Baker until two years ago.
"Early in ... 2000 we learned that two men in Arizona were preparing to sue Baker for past sexual abuse," Mahony wrote. "Once we became aware of that situation, he was removed immediately from all priestly ministry in accordance with the policy in effect at that time."
Mahony did not include in his letter that the archdiocese had received a 14-page letter of complaint that said Baker had continued to molest the two men for 13 years after the priest confessed to the cardinal in 1986. Nor did Mahony mention in the letter that he authorized a $1.3 million settlement with the two men and that the archdiocese insisted the deal remain secret.
The Times obtained a copy of the letter of complaint that was sent to the archdiocese in May 2000 by Tucson attorney Cadigan on behalf of the two men, who are brothers now living in Mexico. The letter of complaint describes the alleged abuses in detail.
At about the same time Mahony returned Baker to ministry in 1987, the two brothers and their mother moved to Guadalajara. According to the letter of complaint, Baker made the first of many trips to Guadalajara to visit the boys in the spring of 1988.
"Baker also flew [the brothers] from Mexico to Los Angeles, Palm Springs and Arizona approximately 15 times and, during the visits to Los Angeles, had the boys sleep with him [in] the rectory, where he molested them," the letter of complaint alleges.
The document also states that Baker provided the brothers with alcohol when they were young minors. The alleged abuses continued until 1999, according to the letter of complaint. The two men said they remained silent because Baker had threatened them if they told anyone and they did not want to hurt their mother, who had befriended the priest and regularly received money from him.