Dylann Roof, 21, was seen in shackles and gray striped prison garb at his first appearance at US District Court in Charleston since his federal indictment on July 22.
He has already been charged by South Carolina with murder over the fatal shooting of nine African-Americans during an evening bible class at Emanuel AME Church in Charleston on June 17.
Defense lawyer David Bruck said Roof was ready to plead guilty, but federal prosecutors have yet to declare if they will seek the death penalty.
"The process has started. This is a long journey, but we are committed to the task to make sure justice is done," Emanuel's interim pastor Norvel Goff told reporters outside the court.
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Roof was arrested in North Carolina the day after the mass shooting whose victims included Emanuel's chief pastor who was also a state senator.
In a website attributed to him, he espoused racist views towards African-Americans and, in photos, posed with firearms and the Confederate battle flag.
He is also charged under a second hate crime law that bans the use of force to prohibit the free exercise of religious belief.
In addition, he stands accused of using a firearm to carry out what Attorney General Loretta Lynch called "racially motivated murders and attempted murders.