The three survivors were were taken to Whatipu Beach where they were treated by Westpac Rescue Paramedics before two were flown to hospital and one taken by ambulance.
It is believed that the victims were in a five-metre boat that was launched from Onehunga and was swamped while crossing the Bar.
They are understood to have been in the water for about two hours before they were spotted by the passing boat, police said.
Police northern communications said emergency services were yet to locate the boat involved in the accident.
Inspector Andrew Brill said: "It could be at the bottom of the ocean. We just don't know yet.''
Mr Brill said police were still looking into the circumstances of the accident and would not reveal any other details - including whether or not those on board had been wearing life jackets.
No details of the people involved were available and their identities would not be released until next of kin had been informed.
Police would investigate the deaths on behalf of the coroner.
