The matter has been referred to the Coroner.
Earlier a North Shore man spoke of his frantic efforts to save the young boy.
Emergency services were alerted to the water emergency at Torpedo Bay Wharf this afternoon.
It is understood that a boy - who an onlooker said was about 5-years-old - had fallen into the water.
Bayswater resident Bernard Riedl said he was walking on the wharf when the boy fell in the water.
"I jumped in to save the boy," he said.
"He put his hands round my neck."
The man said the boy lost his grip as he was trying to rescue him.
"After he detached I couldn't see him," he said.
Coastguard, police, St John and a rescue helicopter were all involved in the emergency response, after an alarm was raised at 3.15pm.
An eye witness said he could see police, Coastguard and a rescue helicopter hovering around the jetty on King Edward Parade.
Police are interviewing several witnesses in the naval museum at Torpedo Bay. One witness said it was too soon to talk about what happened because it was "still raw".
Defence security staff have just moved a small group of hushed onlookers off the approaches to the wharf and on to King Edward Parade.