WASHINGTON (AFP) - A federal judge entered not-guilty pleas Friday for a young white supremacist who is facing hate crime charges over the massacre of nine black churchgoers in South Carolina.

Dylann Roof, 21, was seen in shackles and grey 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.

Defence lawyer David Bruck said Roof was ready to plead guilty, but federal prosecutors have yet to declare if they will seek the death penalty.

Federal magistrate judge Bristow Marchant - who needed almost a half-hour to formally read aloud the 33-count federal indictment - then entered the not-guilty pleas.

"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.

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.

The federal indictment against Roof accuses him of nine murders and three attempted murders under a hate crime law that prohibits the use of force to harm an individual on the basis of race or colour.

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."

Roof's trial on the South Carolina state charges of murder, attempted murder and use of a firearm during a crime is set to begin in July next year.