Dylann Storm Roof was expected to face court later on Friday, accused of gunning down nine African Americans at Charleston's Emanuel African Methodist Episcopal Church.
He is expected to appear by video link from a Charleston detention center to face charges for the killings and for possession of a firearm during a violent crime, the Charleston Police Department said.
The 21-year-old allegedly opened fire at worshippers attending a Bible study meeting at the nearly 200-year-old church on Wednesday night. One day later he was arrested in North Carolina, about 350 kilometers (220 miles) from Charleston, and brought back to South Carolina.
According to law enforcement sources quoted by US media, Roof confessed to the attack and said his goal was to start a race war. He also reportedly told police that he "almost didn't go through with it because everyone was so nice to him," sources told broadcaster NBC, but ultimately, he decided to "go through with his mission."
Roof - whose Facebook page includes a picture of him wearing the flags of former white supremacist regimes in South Africa and Rhodesia - had allegedly complained to a former friend that "blacks were taking over the world."
Joey Meek, who reconnected with the 21-year-old a few weeks ago, said that Roof had declared that "someone needed to do something about it for the white race."
US officials are investigating the attack as a hate crime, which makes it possible to impose additional penalties because of a victim's race, gender or sexual orientation.
Call for death penalty
South Carolina Governor Nikki Haley told NBC on Friday that prosecutors should pursue the death sentence, which is legal in the southern US state.
"We will absolutely want him to have the death penalty," said Haley, a Republican. "This is the worst hate that I've seen and the country has seen in a long time."
"We will fight this and we will fight this as hard as we can," she added.
US President Barack Obama said the shooting stirred up "a dark part" of US history and clearly demonstrated the damage caused by guns in America.
Charleston officials have announced a prayer vigil for Friday evening. Among the nine dead were three pastors - DePayne Middleton Doctor, Sharonda Coleman Singleton and Reverend Daniel Simmons - and Democratic state senator Clementa Pinckney.
The Charleston Emanuel AME Church, founded in 1816 by black worshippers, is one of the oldest black churches in the US South.
nm/sms (Reuters, AFP, AP, dpa)