The explosive allegation comes in the indictment for Jimmy Carlton Winfrey -- the guy busted for firing at Wayne's bus back in April. According to the docs, moments after Winfrey shot up the bus in Atlanta ... he called a phone owned by Birdman.
Adding further suspicion -- after that call, Winfrey drove to the Mandarin Oriental Hotel ... where Wayne's entourage stopped after the shooting. Cops don't say it in the indictment, but the insinuation is Winfrey was told to go finish the job ... but as we reported, police had met Wayne's entourage at the hotel to investigate the shooting.
TMZ broke the story ... Winfrey has been Young Thug's tour manager. Cops also point out that Winfrey is seen brandishing an assault rifle in Thug's "Halftime" music video ... which includes lyrics threatening to shoot Wayne in the head.
Birdman and Thug have not been charged with any crime -- but the indictment makes it clear cops think they're closely tied to the shooter.