Police say they are searching for a suspect who fled the scene. The motive for the shooting remains unclear.
They cordoned off the surrounding streets, according to the Tribune de Geneve.
The men, both Turkish nationals, are believed to be in stable conditions in hospital.
Police have evacuated four people from the building, according to Swiss media. The Langstrasse, a major route in the centre of the city, has now reopened to traffic.
More from the BBC.