It was motoring up the Veronica channel in the Waikare inlet at Opua when the aluminium dinghy with an outboard appeared from its left side.
"So you've got one vessel going up the channel towards the Opua marina and then the other vessel comes from its left across its front, they collided, the male occupant of that dinghy is tossed into the water, [and] his dinghy sinks pretty much straight away."
The dinghy has yet to be recovered and salvage operations will continue today.
The man was unresponsive and floating on the surface of the water after the collision, Mr Le Comte said.
One of the men on the yacht dived in to save the man, who was dragged into another dinghy which the men launched from the yacht.
Crew members from the R. Tucker Thompson ship saw the collision and sent a motorised dinghy of their own to help.
The man was placed in the motorised dinghy and raced back to Opua wharf, while CPR was administered.
Resuscitation attempts continued once the man on shore but he was pronounced dead shortly after.
Police were notifying next of kin, but it was confirmed the man was a local. However, officers are still unsure where he was going in the dinghy.
"It appears that he had a bit of kit on board, there were personal items - clothing, and a pack and chilly bin and all that sort of stuff," Mr Le Comte said. "We're still making inquiries to confirm his movements and plans."
An employee at asset management company Far North Holdings, based at Port Opua, said it had provided footage from its CCTV cameras to Maritime NZ and the police.
The death has been referred to the coroner.
