Earlier reports said five people had died in the crash. Victoria Police later confirmed the number was three, although there were reports that a further passenger was still missing.
Geelong local area commander Inspector Graham Banks said a witness observed the plane crash into the sea.
"Shortly thereafter he called police, water police attended and located what was a large area of wreckage and three deceased persons," he said.
"Currently police are in the process of searching for further wreckage and further other persons involved, although we don`t believe there will be more than one or two person involved at most because we believe the plane was a four-seater plane."
Rescuers in boats and helicopters remain at the scene, with two air ambulances also dispatched to the area.
The township has a small airport but a spokesman for the airport told the Australian Associated Press that all planes from that airport had been accounted for and they didn`t know where the crashed plane had flown from.
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