Reverend Robert L. Brennan, the former associate pastor of a Northeast Philadelphia Catholic parish, has been charged with rape, involuntary deviate sexual intercourse and aggravated indecent assault, the Philadelphia District Attorney’s Office said in a press release Thursday.

Brennan is accused of sexually assaulting an altar boy at Resurrection of Our Lord Parish in Northeast Philadelphia, where he was an assistant pastor, between 1998 and 2001, beginning when the boy was 11, according to the press release.

Brennan, who now lives in Maryland, was arrested by Perryville, Md., police Wednesday, the press release said.

The press release was critical of Monsignor William J. Lynn, the first Catholic Church official in the country to be charged with harming sexual-abuse victims whose abuse he was responsible for investigating.

Lynn was responsible for reviewing allegations of sexual abuse involving priests as the Archdiocese of Philadelphia’s secretary for clergy from 1992 until 2004. He was convicted in June 2012 of endangering the welfare of an abuse victim known as D.G. by his role in assigning D.G.’s abuser — defrocked priest Edward V. Avery, who later pleaded guilty to abusing D.G. — to the parish in which D.G. served as an altar server.

The district attorney’s press release Thursday said Brennan’s case “presents another instance of abuse under the watch of Monsignor Lynn, secretary of clergy under Cardinal Anthony Bevilacqua. The actions Lynn took to shield predator priests from exposure and prosecution led to the victimization of untold numbers of Philadelphia-area children.”

The press release mentioned that in 2005 the archdiocese received word that Brennan had “inappropriately touched” more than 20 boys from the locations where he was assigned.

Reports of the incidents were made by Brennan’s fellow archdiocese employees, including other priests, but the archdiocese allegedly ignored the complaints for more than a decade, the press release said.

Evidence points to a history of misconduct on Brennan’s part dating as far back as 1990, according to the press release, when the principal of St. Pius X High School and the principal of the parish school at St. Mary’s in Schwenksville, Pa., expressed concern about Brennan’s alleged improper behavior with several students.

The press release said that Brennan was removed from his posting at the schools in 1992 when the mother of a seventh-grade altar boy said that Brennan had forced the boy to sit on his lap.

Brennan continued to exhibit sexually abusive behavior toward boys in subsequent assignments, according to the press release, and Lynn, who allegedly heard complaints about Brennan originating from the Resurrection of Our Lord Parish, did not act or recommend to remove Brennan.

Lynn and other archdiocese officials are not being charged with anything in relation to Brennan’s arrest because the victim’s age places his allegations three months beyond the criminal statute of limitations for endangering the welfare of children, the press release said.

Lynn’s own case was argued before the Superior Court on September 17. At that time, Philadelphia Assistant District Attorney Hugh J. Burns Jr. raised the issue of prior bad acts, consisting of evidence of about 21 priests whose files Lynn reviewed as part of his human resources role with the archdiocese.

Burns alleged that the bad acts were probative of Lynn’s experience in supervising priests who sexually abused minors; his knowledge of their tendency to recidivate and the harm they inflict on their victims; and the priorities he served and methods he used to conceal and facilitate their misconduct in a manner that endangered children.

Lynn’s former attorney, Jeffrey M. Lindy, told The Legal on Thursday that Brennan’s arrest won’t have a negative impact on Lynn’s appeal, although, Lindy said, “I think the DA hopes it will … but it has nothing to do with [the appeal].”

In regards to the remarks made about Lynn in the district attorney’s press release, Lindy said, “You can add that as yet one more cynical aspect of the DA’s case against Monsignor Lynn. It’s probably the most cynical prosecution I’ve been part of or observed on either side of the courtroom.”

Lindy said that Lynn should not be considered a supervisor of Brennan from Lynn’s time as secretary of the clergy at the archdiocese, nor should Lynn be deemed responsible for hiding Brennan’s activities.

“Lynn was in the church hierarchy; he had three levels above him that he reported to, therefore anybody below him in the hierarchy reported upward. That doesn’t mean that he was a supervisor of Brennan,” Lindy said.

Lynn’s current attorney, Thomas A. Bergstrom of Buchanan Ingersoll & Rooney, did not return a call seeking comment.

P.J. D’Annunzio can be contacted at 215-557-2315 or Follow him on Twitter @PJDAnnunzioTLI.

Zack Needles can be contacted at 215-557-2493 or Follow him on Twitter @ZNeedlesTLI.