The Diocese of San Bernardino was contacted June 24 by the boys' parents and informed of the alleged abuse.
Father Alex Castillo maintains his innocence and has not been charged with a crime, said John Andrews, spokesman for the diocesan.
"The Diocese of San Bernardino has received information regarding credible allegations of sexual misconduct with minors involving Father Alex Castillo, a priest of our diocese," Andrews said.
This is not the first time a complaint has been made against Castillo, who has been with the diocese since 1988. A complaint from an adult was determined to "not have creditability," Andrews said.
Castillo, who is still a pastor at Our Lady of Guadalupe, is not allowed to have contact with parishioners, Andrews said.
Police were informed of the incident involving the brothers on June 25.
Ontario police Sgt. David McBride said Castillo has not been charged. McBride said he could not provide more information on the incident because the investigation - which started in early July - is ongoing.
The diocese has their own review board that investigates abuse allegations. The board has met twice since the allegations surfaced, Andrews said.
After the allegations were found to be credible, the diocese and Bishop Gerald Barnes decided to publicly announce the allegations, Andrews said.
"We are very saddened by these allegations," Andrews said. "Any acts of abuse against a child is unacceptable, criminal and a sin in the eyes of our faith."
But David Clohessy, national director of St Louis-based Survivors Network of those Abused by Priests, contends the case has not been handled correctly.
"They are handling it terribly. Since 2002, the Catholic Church has pledged to be open and transparent on child sex abuse cases, they obviously are not," Clohessy said. "It's just irresponsible to keep a serious allegation confidential from the public."
The Survivors Network of those Abused by Priests is one of the oldest and largest support groups for clergy abuse victims.
But, Andrews said, the church has changed its policies and procedures to prevent abuse.
The letters sent out by the diocese about the allegations against Castillo were read this weekend at Our Lady of Guadalupe and St. George Catholic Parish, also in Ontario. They were also read at St. Catherine of Siena in Rialto and St. Anthony in San Bernardino. Castillo has served as a pastor at those parishes.
Castillo joined the diocese in 1988, serving with St. Anthony Parish in San Bernardino. From 1991 through 1996, Castillo worked in the diocese's Pastoral Center in Ministry.
In 1996, he left the diocesan to work for the Sacramento-based California Catholic Conference, a state organization that represents bishops.
Castillo was with the conference until 2000 when he returned to San Bernardino.
He was a priest at St Catherine of Siena Parish in Rialto Catherine of Siena for three years. In 2003, Castillo moved to Our Lady of Guadalupe. He also served as priest at St. George from 2006 to 2008, Andrews said.
Earlier this summer, Castillo signed a letter that started a recent squabble over Arizona's immigration law. He sent a letter to Mayor Paul Leon urging the City Council to publicly oppose Arizona Senate Bill 1070. The illegal immigration enforcement law is considered the country's broadest and strictest anti-illegal immigration measure in decades.
The letter was sent on behalf of Our Lady of Guadalupe Church parishioners and included a request for a public meeting with council members to discuss the law.
The request drew the ire of Claremont-based We the People, California's Crusaders, which asked the council to pass a resolution supporting the law. The City Council on Sept. 7 decided to not get involved in the debate.
Anyone who may have been abused by Castillo or any other church personnel, can call the diocese's abuse report hotline at 888-206-9090.
The Ontario Police Department is encouraging victims to call Detective Mark Guski at 909-395-2726.