The man, whose name has not been released, had been with two male companions in a three-metre dinghy that left Kananook Creek about 10pm on Friday.

Mornington police were told by the two survivors that the boat capsized and sank in choppy waters near Daveys Bay at Mt Eliza about 11.30pm. They said they were able to make it to shore, searched along the beach for the man then made their way to Frankston and called the police.

A search involving water police, police air wing, Coast Guard, Volunteer Marine Rescue Mornington and Frankston SES was conducted around Daveys and Canadian bays.

Members of the missing man's family were at the search base at Daveys Bay beach.

The wind on Saturday morning and afternoon was from a northerly direction. The boat was found on Saturday afternoon two kilometres offshore from Sunnyside Beach, three kilometres south-west of Daveys Bay.

Early on Sunday morning the wind shifted to a westerly.

On Sunday afternoon, before the body was found, the officer in charge of the investigation, Detective Sergeant Peter Webster of Mornington CIU, said he did not believe there were suspicious circumstances.