Officials said that the fire started as people sought shelter in the station from the two days of torrential rainfall in the city that has left many homeless and without power.
There are fears that the death toll from the fire could rise as the search for bodies continues.
President John Mahama has visited the burnt-out petrol station and has appealed for calm as authorities try to cope with the aftermath of the fire and heavy rain.
Reports says there are chaotic scenes in the city with cars being carried away by the water and many roads blocked off.
A victim told a local radio station that he had put his children on top of a wardrobe to save them from the water coming into his house.
Weather forecasters in the meantime have said that more rain is on its way.