The two remaining men were whipped by strong winds of up to 20 knots and pelted with rain as they waited four hours on the remote Fiordland coastline for help.
One of the men did not survive.
As darkness fell, the third member of the group pushed his way through rough, rugged terrain to seek help, eventually raising the alarm at the remote Waitutu Lodge, 2km away.
Sergeant Tod Hollebon, of Te Anau, said the three men had left the Waitutu River and were heading about 12km around the southern coast to the mouth of the Wairaurahiri River when the boat was swamped.
The men were thrown into water about 1km west of the Wairaurahiri River mouth, on the south coast, between 3pm and 4pm.
It is understood they spent about an hour in the sea.
Due to the remote and rugged location, it took another three to four hours for one of them to raise the alarm.
With no cellphone reception, the managers at Waitutu Lodge radioed the closest rural town, Tuatapere, and police were contacted at 7.15pm.
Te Anau-based Southern Lakes Helicopters flew a paramedic and a police officer to rescue the other two men.
Sgt Hollebon, who was the police officer on board, said they were able to quickly locate the two men still on the coastline.
On arrival they found one of them had died and the other was freezing from sitting in the bitterly cold conditions.
The helicopter picked up the survivor on the coastline and the other survivor, who was being cared for at Waitutu Lodge, and took them to Southland Hospital, in Invercargill.
"They were very cold and had clearly suffered an ordeal. Quite exhausted, actually. They have done really well to get through that."
A second helicopter was called to transport the body.
The men, from the South Island, had been visiting Fiordland National Park. The only access to the area where they were is a walking track, or by jet-boat or helicopter.
They had been travelling as part of a larger group with three jet-boats in total.
However, the other jet-boats were not with them when the boat flipped and had been unaware they were in trouble.
Police were still making inquiries into what the group had been doing in the area and what caused the vessel to capsize.
Sgt Hollebon praised the lodge managers for their help and said if the third occupant of the boat had not gone for assistance they could still be missing.
"He did well to find his way back to the lodge and raise the alarm and assisted in saving the survivor - the person left at the scene," he said. - NZME
