PROVIDENCE, R.I. — A Roman Catholic priest placed on leave last year after allegations that he sexually abused children was charged Friday with sexually assaulting two people in the 1980s and 1990s at churches in Cranston and Providence.

Barry Meehan, 65, of West Warwick pleaded not guilty to five counts of first-degree sexual assault.

He resigned as pastor of St. Timothy’s Church in Warwick in January 2013 and was placed on administrative leave by the Diocese of Providence. The diocese said Friday that it took action “after credible allegations of sexual misconduct with minors were received.”

Meehan’s lawyer, Kevin Bristow, did not comment after Friday’s court hearing.

The diocese said in a statement that it had alerted the Vatican about the allegations. It said Bishop Thomas Tobin has asked that Meehan be permanently removed from the priesthood and the Vatican is reviewing his status. Meehan’s permission to function as a priest was removed last year.

The attorney general’s office said a statewide grand jury indicted Meehan on Wednesday on charges he assaulted a male older than 14 while assigned to St. Mary Parish in Cranston between April 17, 1986, and Jan. 25, 1991. He is also accused of assaulting a different male older than 14 at St. Augustine in Providence between Jan. 25, 1991, and Aug. 31, 1992.

Meehan was arrested Thursday, police said.

State police said the diocese reported allegations in December 2012 that Meehan had sexually assaulted several young people, and they conducted a joint investigation with the diocese. Police said the investigation is ongoing.

“I commend these individuals for coming forward and placing their confidence and trust in the criminal justice system,” Col. Steven O’Donnell said.

Meehan was released on $50,000 bail with surety, ordered to surrender his passport and scheduled to be back in court Dec. 11 for a pretrial conference.

The diocese said Meehan was ordained in 1978. He also served at three parishes in West Warwick: Sts. Peter & Paul, St. John the Baptist and St. James.