The man was shot outside of the concert venue Loppen, located between Christiania's two main entrances.
Police responded to the shooting in large numbers and closed off the area, including the street Prinsessegade which runs across the former hippie commune's entrances.
The shooting occurred shortly after 9pm and as of Monday morning no arrest had been reported.
The incident follows a series of recent shootings in the Copenhagen area, including on Saturday night when two men where injured in the Tingbjerg neighbourhood.
Police have said that at least some of the shootings are thought to be connected to gang clashes.
Two of the incidents were fatal, with a 30-year-old man killed in an October 7th shooting near Hans Knudsens Plads in Østerbro and a 21-year-old dying from injuries he suffered in an October 2nd shooting in the Emdrup neighbourhood.
Sunday's incident was also the second shooting in Christiania in recent months. Two police officers and one civilian were shot on August 31st in an incident that led to renewed attempts to shut down the area's open-air cannabis market known as Pusher Street.
The gunman in that shooting was killed by police in an exchange of fire. One officer was seriously injured but is now out of critical condition. The other two victims escaped serious injuries.