Some mourners attending the funeral of Rev. Howard Creecy, Jr. took offense to the flag flying above a monument for Confederate soldiers, about 400 of whom are buried in the cemetery as well. Creecy was the president of the Southern Christian Leadership Conference, an organization co-founded by Martin Luther King, Jr.
A flagpole in the cemetery flies both an early version of the Confederate flag and one with the stars-and-bars design.
On Wednesday, protestors upset over the flag called for its removal.
"For me, it is just an affront to everything that has happened for civil rights and justice for all people that are concerned that the flag still hangs," protestor John H. Lewis told Atlanta's WAGA-TV.
Rev. Benford Stellmacher told the station many people came to him upset and asked him to do something.
"We're prepared to climb up there and take it down, but we want to do it in the spirit of and the cooperation of Christ," Stellmacher said.
Cemetery officials said while they understand the complaints, they can't remove the flags because a Confederate veterans group purchased the rights to build and maintain the memorial years ago.
"I have no control over that, it is a memorial with 400 burials underneath," Charles Bowen, Jr. of the cemetery told WAGA-TV.
The Songs of Confederate Veterans group said they will not remove the flags.
"Those flags have flown there for many years and will continue to fly there for many years honoring our Confederate heroes and our Confederate dead. It is not a racial issue," the group told WAGA-TV.
A representative from the SCLC said the organization itself does not have a major problem with the flag's presence, as it does not fly over the entire cemetery.