The Rev. Jose Chavarin apparently left after officials with the Archdiocese of San Francisco, where he's worked for 11 years, confronted him about the allegations, diocese spokesman Maurice Healy said.
The diocese later received two phone calls claiming Chavarin was in his native Mexico, Healy said.
The Diocese of San Diego first learned of Chavarin's alleged sex abuse on June 20, the same day it alerted authorities and San Francisco church officials, according to its spokesman, Chancellor Rodrigo Valdivia.
California law mandates that the church notify law enforcement or Child Protective Services of the alleged abuse to minors within 24 hours of learning it.
Healy said Chavarin, 59, denied the accusations and was placed on administrative leave. The diocese also told him not to leave town, even though Chavarin said he wanted to visit relatives.
Three days later, the diocese received a voicemail from someone claiming to be Chavarin's friend saying the priest was killed in a car crash in Mexico. The same person called later saying that Chavarin was alive in Mexico and planned to return, according to the diocese.
Charles Smith, a spokesman at the U.S. consulate in Tijuana, said authorities there were investigating but so far had uncovered no information.
Monica Munoz, a spokeswoman for the San Diego police department, said they received a letter on July 2 from an attorney who represents two people who claimed they were abused by Chavarin between 1986 and 1991.
Munoz said police are in contact with the attorney, whom police would not name, and that the attorney is encouraging the victims to come forward.
Chavarin is a canon lawyer who for the past six months had been in Rome studying law and has worked in the diocese's Metropolitan Tribunal, where married couples apply to get annulments.
Healy said no allegations against Chavarin have surfaced in San Francisco.
In September, the San Diego diocese reached a $198 million settlement with 144 people who claimed they were abused by clergy as children.
The diocese avoided civil litigation by filing for bankruptcy in February 2007 on the eve of the first trial. It released names of accused priests in March 2007, but that list did not include Chavarin.
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