The warden was attacked as he parked his bicycle under a shelter in front of the prison before beginning his night shift.
He was then ordered to lie on the ground before being hit by shots.
Danish Prison Service (Fængselsforbund) chairman Kim Østerbye told Jyllands-Posten that the warden had been hit three times, athough Funen Police were unable to confirm the exact number.
"I can confirm that he was hit more than once," duty officer Steen Nyland told the newspaper.
After the masked gunman fired the shots, he ran towards a black car that was parked nearby. Three other people were waiting in the car, Funen Police said via a statement.
Shortly before 11pm Tuesday night a torched car was found on Hjulbyvej, just south of the main Funen motorway. The burned car, an Opel Astra, was stolen nearby on the 11th or 12th of July, according to the police statement.
The injured warden is in a stable condition in hospital and is awaiting surgery.
No information was available on the type of weapon used, writes Jyllands-Posten.
"I see this purely as an act of revenge," Østerbye told the newspaper.
"I am personally convinced that they [the perpetrators, ed.] are from the underground crime scene. There is no doubt that they are trying to take hold of power in certain prisons and certain sections," the prison service chief continued.
In addition to last night's shooting, Østerbye said that two separate knife attacks and two attempted murders on wardens had taken place within the last six months.
Nyland told Jyllands-Posten that police were including the underground crime scene in their investigation into the incident.
"We will be out making many inquiries in the area, and we hope that someone will have seen something we can work with," said Nyland.