A pastor from Sellersburg, Indiana, and a fellow church worker are facing felony battery and neglect charges after they were accused of severely beating several children under their care using a wooden paddle.

Crossroads Baptist Church Pastor Gerald Harris operates a boarding academy in Clark county that includes dormitories and classrooms for out-of-state students aged eight to 19 years old.

Clark County Prosecuting Attorney Jeremy Mull said authorities arrested Harris, 47, and church employee Christopher Williams, 21, last week after several students filed complaints that they have been subjected to "various forms of punishment" by the two accused.

Mull said it is okay for the children to be disciplined "in a legal way," but the bruises on the children's bodies showed they received a kind of "punishment" that can be considered as criminal abuse.

"That's the point where, in my opinion as a prosecutor, it crosses the line from appropriate discipline to a criminal battery," Mull said.

Harris and Williams both live inside the church.

Interviewed by the Clarksville police and Child Protective Services, the victimised children said they were whipped with a wooden paddle.

An eight-year-old boy said Williams tied a rope around his waist and jerked him around "for not behaving."

An 11-year-old boy with "very serious bruising" on his buttocks and legs said he was whipped using a paddle by both Williams and Harris as punishment for wetting his bed.

Another student testified that Harris and Williams even made one 16-year-old teen stand before the other boys as they repeatedly whipped him. The teen's "crime"? He smirked at Harris after he was told to keep reading the Bible, the student witness said.

Those weren't the only forms of abuse they were subjected to, the children said. They also revealed that they were not allowed to use the bathroom once the lights were turned off.

The Clarksville Police said they first got a hint of the child abuse going on inside the boarding academy after one of the children who was selling candy bars admitted to his customer that he feared he would be whipped and punished if he did not sell enough candy.

All of the children have already been removed from church custody and are now back with their parents or under Clarksville's Child Protective Custody.