A maintenance worker discovered the flags early on Thursday morning at the Ebenezer Baptist Church.
There has been a campaign to remove the flag from public life after it was brandished by a white suspect who it's alleged killed nine black Christians at a church in Charleston.
The flag was flown by armies of the pro-slavery Confederacy during the Civil War and is claimed by some white southerners as a symbol of regional and ancestral pride.
It has also been used by white supremacists and is seen by many African-Americans as a symbol of oppression.
At a press conference, pictured above, police said they were investigating but there are no witnesses.
A security guard saw a suspicious vehicle across the street from the church on Wednesday night, but it was not clear if it was related.
Martin Luther King once preached at the historic Ebenezer Baptist Church, which is near the new church where the congregation now meets and where the flags were placed.