There was no immediate information on potential victims.
The shooting took place at the Emanuel African Methodist Episcopal (AME) Church, said State Rep. Wendell G. Gilliard who represents the district where the church is located.
On its website, the church describes itself as the "oldest AME church in the south."
Gilliard didn't have additional information and said he was on his way to the scene.
Police too have offered little information. The department listed the site of the shooting as 110 Calhoun Street, the location of the church.
The department said the suspect in the shooting is a clean-shaven white man in his 20s, with a slender build. He was wearing a grey sweatshirt, blue jeans and boots.
Soon afterward, news camera showed officers taking a man matching that description into custody -- but police said they were still looking for the shooter.
Every Wednesday evening, the church holds a Bible study in its basement.
Corey Wessenger, who was standing across the street from the church, said the area was swarming with a heavy law enforcement presence.
"I just saw a group of about 40 people escorted by cops," Wessenger told CNN by phone.
Patrick Wright, a reporter with WFMY News, tweeted, "We've been told not to leave our restaurant here in #Charleston for the time being. Helicopter still circling above."
According to USAtoday.com, multiple people are dead but it has not been confirmed how many yet.
NewsChannel 3 will continue to post more updates as we learn more.