The charges stemmed from a two-year grand jury investigation into priest abuse in the Archdiocese of Philadelphia, the second such inquiry in the city.
In the rare, if not unprecedented, move, the grand jury charged Monsignor William Lynn with endangering children in his role as secretary for clergy under former Cardinal Anthony Bevilacqua.
Lynn, 60, had a duty to protect children in the five-county archdiocese and refer priests with known sexual problems for rehabilitation or prosecution, District Attorney Seth Williams said in announcing the charges.
"He instead lied to parishioners and went out of his way to reassign priests without telling pastors or principals . that they were pedophiles," Williams said.
Lynn's defense lawyer said the two endangerment counts should not apply because Lynn did not have any children under his care. He also questioned the merits of the charges, which carry a maximum 14-year prison term.
"We certainly don't concede for a moment that he knew he was putting children at risk," lawyer Tom Bergstrom told The Associated Press.
The current case, referred by the archdiocese, involves two victims, one of them a boy who was allegedly abused by two priests and his sixth-grade teacher at St. Jerome Parish, starting when he was a 10-year-old altar boy in 1998.
The other victim was a 14-year-old boy abused by another priest who previously served in the same parish and had a prior history of impropriety with minors, the report said.
Lynn figured prominently in a scathing 2005 grand jury report that found 63 priests in the archdiocese had been credibly accused of child sexual assault over several decades while local church officials turned a blind eye. Frustrated prosecutors then concluded, though, that they could not file any criminal charges because the statute of limitations on the crimes had expired.
Pennsylvania has since revised laws to give child sex-assault victims more time to report abuse, while the archdiocese under Cardinal Justin Rigali has pledged to refer credible complaints to law enforcement.