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The 80-year-old man s body has been recovered and police confirmed they are investigating the incident.
Shortly after it is understood police were also alerted to a boat fire about a kilometre off the shore of Quindalup in Geographe Bay, south of Rottnest Island, in a separate incident.
There have also been reports of a fatality in a yet another incident near a boat in the water off the coast of Hillarys, north of Perth, on Saturday morning.
Fremantle Volunteer Sea Rescue told Daily Mail Australia they were first on the scene of the collision and assisted the injured man.