Shocking footage from the gig showed hundreds of people running from the scene.
Police confirmed 12 fans were injured following but have said they could not find evidence of a shooting at the scene.
The rapper was only three songs into his set when he was said to have been led off stage by security.
Officials at the Atlanta police department said someone in the crowd yelled that they heard gunshots, WSB-TV reports.
They say people were left with ankle injuries and cuts from attempting to jump fences.
Lil Wayne was performing as part of the A3C Hip Hop Festival and Conference in Atlanta.
He later tweeted: "Hope everyone at A3C is safe!!"
One fan tweeted: "Sad ending to A3C. Always such a positive environment and Wayne sounded great until everyone started running. Have a feeling it was a fight that people overreacted to."
Atlanta Police Department confirmed it was sparked by a person in the crowd.
They told The Fader: "It appears that someone in the crowd yelled that they heard gunshots.
"This caused people at the event to attempt to flee the location. There have been approximately 12 minor injuries reported to police such as ankle injuries and lacerations from attempting to jump fences.
"At this time we have been unable to locate any evidence to support claims that shots were fired.
"The event location is being cleared out by police at this time. The investigation continues."
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