MILTON — An arrest warrant has been issued for the missing Rev. Jose “Joe” Rosa, alleging he had indecent sexual contact with two boys at his Valley home and at Congregacion Menonita Shalom Church in New Columbia, state police at Milton said Wednesday.

A cloud of suspicion has hung over Rosa, 52, of 1104 Sabra Way in Kelly Township, Union County, since his disappearance May 21.

“We don’t know (Rosa’s whereabouts), but we have to move this along,” trooper Matt Burrows said of the filing of criminal charges.

Court documents filed by trooper Patrick Beaver provide some insight into the events that led to a warrant being issued for the pastor’s arrest.

They show that Rosa was reported missing only minutes after a high-ranking church official informed state police about the alleged sexual abuse.

It was 8 p.m. Saturday, May 23, when Bishop Samuel Lopez, administrator of the Spanish Mennonite Council of Churches that oversees Congregacion Menonita Shalom Church, told police the council had received a letter from a young male, a former church member who had since returned to Puerto Rico, claiming Rosa had touched him inappropriately, court documents said.

Lopez also provided police a list of individuals and contact information for people who could “likely provide more details regarding this and other complaints against Rosa,” the complaint said.

At 9:30 that same night, just after police received the complaint from Lopez, Rosa’s wife, Maggie, reported her husband was missing and hadn’t been seen in two days.

There has been no sign of Rosa since he was last seen by a neighbor around 11 a.m. May 21, walking from his home toward the U.S. Penitentiary at Lewisburg, police said.

Trooper Beaver said in court documents that he was unable to contact the boy who wrote the accusatory letter because he had left for Puerto Rico.

However, Beaver did interview two other boys, both 14, who claim they were sexually abused by Rosa after moving in temporarily with his family at 1104 Sabra Way in 2005.

The alleged victims, 9 and 10 in 2005, described a similar scenario of being touched inappropriately and being pressured to sleep in the same bed as Rosa at his home.

The younger boy said Rosa kissed him on the lips and grabbed his buttocks inside the church. The abuse ended early this year when his family stopped attending the church, court documents said.

The other boy said he and his family lived in the Rosa home for two months in 2005, and during the next two years, Rosa touched his genitals on 10 or more occasions whenever they were alone in the house.

Rosa was a pastor in Lancaster before moving to the Valley seven years ago to take over as spiritual leader at Congregacion Menonita Shalom Church.