Save Southern Heritage claimed responsibility on social media for flying the Confederate symbol above the Florida city for the second time in a month.
The activist group, which opposes efforts to eliminate Confederate monuments from Jacksonville, also sent a message to mayor Lenny Curry with the banner, “Curry, stop your hate!”
Florida Politics reported that staff at Jacksonville’s City Hall discovered bullet holes in a window close to Mr Curry’s office at the same time the plane was circling overhead.
Save Southern Heritage spokesperson told The Independent via email they were not responsibe for the bullet holes.
The group sparked outrage from NFL fans when it flew a Confederate flag over TIAA Bank Field during a game between the Jacksonville Jaguars and Baltimore Ravens on 27 November, Action News Jax reported.
At the time, Mr Curry tweeted that there was “no place for hate of any kind in our city”.
“My position on monuments remains clear: I have allocated money for removal and empowered city council to take action,” he wrote.
Florida Governor Ron DeSantis refused to condemn the action, instead blaming the media for taking “some jabroni that nobody cares about” and making them a “celebrity”.
In late October, an unknown group displayed anti-semitic messages at the stadium and onto highway overpasses ahead of the high-profile Florida-Georgia college football game.
Like many cities in the southern United States, Jacksonville leaders have been wrestling with abolishing Confederate statues fro some time.
The city rejected a $500,000 funding application to remove Confederate monuments in June, Florida Politics reported.