The half-dozen small flags were placed overnight by the unidentified suspects at different locations around the Ebenezer Baptist Church, which is contiguous to The Martin Luther King Jr Center for Nonviolent Social Change in Atlanta.
"We do have images of two white males placing those flags," Atlanta Police Chief George Turner told reporters.
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The Civil War banner, an emblem of the slave-owning South and seen by many now as a white supremacist symbol, has become a focus of an intense debate on racism in America since last month's killing of nine black worshippers at a Charleston church.
The suspect in the massacre, Dylann Roof, had posted a picture of himself holding the Confederate flag and a handgun.
Ebenezer Baptist Church's senior pastor Raphael Warnock said the sight of the flags in his church was "disturbing and sickening, but unfortunately not terribly surprising."
"We have seen this kind of ugliness before, not just in the 1960s but in recent years, we've received calls in recent weeks, threatening calls with severe racialized language and slurs.
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