The dead man's family and the owners of the chartered vessel, Mark and Denise Barnes, yesterday took part in an emotional Maori blessing.
Coastguard operations manager Ray Burge said the severely injured diver was unconscious but still breathing when he was pulled from the water.
By the time a rescue helicopter paramedic was winched on board the man had died.
Police are conducting an investigation on behalf of the coroner.
Another member of the West Auckland club said it was a scheduled club dive and about 12 members signed up to dive for three days around the island group.
Dive Tutukaka spokeswoman Kate Malcom said the experienced dive club member was on the surface of the water at Landing Bay Pinnacle when the accident happened.
"This is a boating incident rather than a diving incident."
Maritime NZ rules oblige skippers and divers to keep a lookout at all times, travel at a safe speed, display an A (alpha) flag to indicate that a diver is in the water, move at under five knots, and keep 50m from other vessels.
Maritime NZ said it has previously investigated accidents where swimmers, spearfishers and divers have been hurt by vessels operating in excess of five knots within 200m of the shore.
In 2004, a diver was run over by a boat near Kawau Island in almost identical circumstances.