Both the pastor, Jerry Harris, 47, and a school employee, Christopher Williams, 21, were arrested at Crossroads Baptist Church Tuesday afternoon and charged with battery and neglect.
Clarksville Police said Wednesday they were continuing to investigate and interview students and school staff members.
Police say the school had 8 full time employees and more charges are possible.
The school, according to police, houses 23 young men from across the country, ages 8 to 18, who were sent to the school after disciplinary issues.
Clarksville police say several students had marks on their bodies consistent with abuse and one told authorities he had been hit with a paddle.
The investigation began Monday in Owensboro, Kentucky.
The group had been stopped for selling candy bars without a permit.
Also on Monday, according to the Owensboro Police Department, one of the students was arrested after he groped a woman shopping at an area mall.
Police won't say what led them to contact Clarksville authorities, but were happy to get the ball rolling on the investigation.
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Mull said he currently knows little about the school, such as when it began operations, how out-of-state parents found out about the school or how many total students attended. "We're looking at exactly what the arrangements were for keeping the kids, what the philosophy was, what the reasonings were for kids being here," Mull said.S. Ind. boarding school employee arraigned
According to the school's Facebook page, the Well of Grace Boarding Academy "is a boys home under the authority of Crossroads Baptist Church."
Its stated goals include "reaching school age boys heading down the paths of destruction" and "watching the transformation of unwanted, and seemingly ruined lives into Godly young men."
Mull said the academy, located on the property of Crossroads Baptist Church, provided the children with educational curriculum as well as meals and a place to sleep. Many of the children are from out of state and a big part of Thursday was getting them back home.
"The Clarksville Police Department and the Indiana Department of Child Services is working with the parents of the children to arrange for their transportation back,” Mull said.
Mull said caretakers and teachers in Indiana have a right to spank children when appropriate, but some of the discipline that happened at Well of Grace Boarding Academy--including the use of a wooden paddle--crossed the line.