The shooter is still at large.
The shooting took place Wednesday evening at the Emanuel African Methodist Episcopal Church, the oldest AME church in the South.
Police haven't said how many people have been shot. But the source who spoke to CNN said several bodies were in the church that were yet to be identified.
"It's really bad. It's a very bad scene," local pastor Thomas Dixon said.
"Apparently the person just entered the church and opened fire. That part has not been fully articulated on what happened yet ... they are still looking for the suspect."
Search on for suspect
Police said the suspect in the shooting is a clean-shaven white man in his 20s, with a slender build. He was wearing a gray sweatshirt, blue jeans and boots.
Soon afterward, news cameras showed officers taking a man matching that description into custody, but police said they were still looking for the shooter.
The department asked anyone with information to call 911 dispatchers