Emergency services were unsure whether anyone was on the boat when it capsized.
Police have deployed a drone over Henderson Cliffs Lookout to search for anyone who may have been onboard the vessel when it sank.
A helicopter and water police vessel have also been deployed to assist with the search but were forced to abandon the search due to heavy smoke.
Police Divers are now searching Cockburn sound for the boat which police hope will help them to identify the owner.
A search of the shoreline along Henderson Cliff Lookout will commence when State Emergency Services arrive at the scene.
Police are asking anyone with information about the boat or its owner to contact Crime Stoppers on 1800 333 000.
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