The 26-year-old man was hit in the upper arm and the chest, and the police report said that the officer was acting in self defence.
Police were called to an apartment building in Salzburg's Gnigl district at around 1.00 am after a resident heard suspicious noises coming from the basement.
Police secured the outside of the building and two officers went down to the basement.
The first officer said in a statement that he spotted a man, who ran towards him with a screwdriver in his raised hand. He then shot at the 26-year-old man, who fell to the ground. The officers immediately called an ambulance.
The police report said that the man was never in mortal danger. The suspected burglar and the police officer are both the subject of an ongoing investigation.
According to a report in the Salzburger Nachrichten a copy shop on the ground floor of the building had been broken into several times during the past few years.
A door inside the copy shop led to the basement, which had since been secured, and the suspected burglar must have made a noise when he forced it open.