Police confirmed an operation was under way in a street close to the city's main station.
Swiss reports said the three wounded were all adults who had been found in Eisgasse, a small street where an Islamic centre is based.
There was no indication who carried out the shooting but local media said the attacker had fled the scene.
It was unclear if the Islamic Centre was targeted in the attack, which took place shortly before 17:30 (16:30 GMT) on Monday.
Police cordoned off the centre as they searched the building, reports said.
Three people have been hurt in a gun attack near a Muslim prayer centre in the Swiss city of Zurich.