A northern fire communications spokesman said the fire happened at the site on Causeway Rd, Ostend. There are numerous boats in the area, some undergoing repairs.
Waiheke Boating Club commodore Gerry Morgan said the fire occurred on a "live-aboard" situated near the high-tide mark on the beach near Ostend.
"It's nothing really to do with the boat club.
"They just pull up on the beach. They've been there for years - a lot of old derelict boats and there's quite a few people living on them.
"There's some houseboats further around the beach, there's respectable people living on those, but there's some real characters living on some of the other boats."
The boat was believed to have been owned by a man who had lived on his boat at the island for at least 10 years and had previously lost another boat to fire, Mr Morgan said.
"It's his friend I believe that's died....he normally lives on his own but there's quite a few live-aboards which get together get together and have a few drinks and that from time to time."
Auckland Rescue Helicopter Trust crewman Ati Wynyard said they were alerted to the fire around 9.45pm last night.
"We had one status 1 [critical] patient and there was one person missing.
The crew landed at Surfdale School to airlift a man with extensive burns to Middlemore Hospital, Mr Wynyard said.
"25 to 30 per cent of his body was burnt. We have no idea whether it was an explosion on the boat, or whether it was just a fire."
Fire investigators were due to arrive at the scene this morning and more police staff had been sent from Auckland to conduct the investigation.
Steve Alloway, publicity officer for the Waiheke Boating Club said the burnt launch had been dragged to shore this morning and covered with a tarpaulin and looked "shot to bits".