The Joint Rescue Coordination Centre in Victoria says an empty six-metre pleasure craft was spotted in Howe Sound near the island on Saturday night around 9:30 p.m. PT.
No one was aboard the vessel, even though the keys were still in the ignition and the motor was in the water.
Lt. Paul Trenholm said search crews found the body of the girl floating near Brigade Bay around two hours later.
RCMP officers said they believe she had been on the boat with her father, a 60 year-old man from North Vancouver.
Rescue teams are still searching for him and RCMP are investigating the incident while the Coroners Service is working to determine the girl's cause of death.
"While there is no indication of foul play at this time, we have not ruled anything out and are working diligently to try to find out what happened," said Const. Harrison Mohr with Sunshine Coast RCMP.
"This is an unimaginable tragedy, and our deepest sympathies go out to the family and friends of this girl and her father."
Police said anyone who saw the beige, six-metre hard-top boat between Lions Bay and Gambier Island late Saturday afternoon should contact RCMP at (604) 885-2266.