Dylann Roof is being held at Charleston County jail, the same facility as Michael Slager, the police officer who killed Walter Scott, the Charleston Post and Courier reported.
A previous version of this story was misreported, saying the two were in adjacent jail cells. They are just being held in the same facility.
Mr Roof is set to appear in court on Friday and has been charged with nine counts of murder after allegedly opening fire on parishioners at the Mother Emanuel AME Church.
He was arrested in Shelby, North Carolina on Thursday and was flown back to Charleston to face charges.
Mr Slager has been jailed for weeks following the 4 April shooting of Mr Scott, a 50-year-old black man, who died after being shot while running from the officer.
The death of Mr Scott exposed racial tensions in Charleston that have been exacerbated after the church massacre. Emanuel AME Church is a historically black church.
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