Rescue workers were still clearing the rubble and debris of the collapsed roof and searching for survivors in Karachi's Malir area.
A rescue official said that apparently a huge water tank placed on the roof of the mosque had caused the cave-in as the roof was not constructed with proper material.
The incident happened when people were praying in the Madina mosque.
In June in another similar incident six worshippers were killed when the roof of a mosque collapsed after Friday prayers.