The men were rescued in treacherous waters at Point Lonsdale on Thursday night.
The trio abandoned the boat to stand up on rocks for two hours in four-metre swells before being picked up.
Water Police inspector James Dalton said they were “in absolute grave danger.
”We were able to get a rope to them and eventually tow the life raft into deeper water,” Dalton said.
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Their million-dollar Port Phillip Sea Pilots fibreglass vessel was smashed into pieces and may take several days to clean up.
“As to what exactly went wrong there and why they ended up there, we’re just not sure yet,” Port Phillip Sea Pilots Jon Dicker said.
The crew were uninjured and an investigation is underway.