The accident took place in the stretch of sea between Xlendi and Dwejra at 5.15pm.
The Armed Forces of Malta was called for assistance to rescue the three men who were on the boat.
The men, all aged 29 and who reside in Xewkija, Luqa and Siggiewi, were lifted onto an AFM dinghy and taken to the Gozo General Hospital for treatment.
The man from Xewkija was found to be suffering from serious injuries.
Magistrate Paul Coppini is leading an inquiry.