"At least five people are reported to have been on board the boat and have evacuated the craft. All were wearing life jackets.
"Emergency services are in attendance, including Deodar, the Auckland Maritime Unit."
The fire was thought to have been started in the engine room, the spokeswoman said.
Lincoln Davies, the helicopter service's communication manager, said a crew flew to Waiheke Island at around 7.15am to help a man, aged in his 40s who had suffered smoke inhalation in the boat fire.
Two children were among the five people on the boat.
"The two children and two adults went to shore by dinghy.
"The patient we treated [had] stayed to try and extinguish the fire before he swam to shore.
"The fire is believed to have been started when the engine key was turned on. He was flown to Auckland City Hospital in a moderate condition."
Witness Cameron May said he had launched from Waiheke Island this morning on a fishing trip when he saw the boat ablaze in Hooks Bay.
The Deodar police boat and the rescue chopper had not yet arrived, but there was another boat moored nearby and a runabout that had gone to check on the occupants of the vessel that had been on fire, he said.
"The occupants were on the beach just sitting there watching it burn because there was nothing they can do," he said.
"Then within a couple of minutes of us arriving the helicopter showed up and the Deodar came around the corner."
May said he could see three people on the shore at the time.
A Fire and Emergency NZ spokesman had said earlier that his team were on their way to a fire but he couldn't confirm the details of the blaze.