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Fisheries observer Martin Bowers, 47, had his arm yanked from its socket and his forearm mutilated when his lifejacket became snagged on a conveyor belt on a Korean fishing vessel on Friday night.
His dislocated shoulder had to be put back into place, while his forearm had to be amputated below the elbow.
Maritime New Zealand (MNZ) has launched an investigation into the accident, about 105km southeast of Bluff, about 8.30pm on Friday.
Spokesman Steve Rendle said the Korean-flagged vessel Sur Est 700 had berthed in Timaru and investigators had begun their inquiry this morning.
It was not known how long the investigation would take.
"We'll be talking to the crew obviously, and in due course, the injured person. So that's obviously going to take a bit of time, so it's difficult to put a time frame on it."
The vessel was foreign-flagged, which meant New Zealand's health and safety laws did not apply to the ship - but Mr Bowers' employer, the Ministry for Primary Industries (MPI), was bound by the health and safety laws.
The Maritime Transport Act also applied to the vessel.
Language was understood to be a difficulty when organising Mr Bowers' rescue, but Mr Rendle said if language was an issue for investigators then "necessary steps" would be taken.
Helicopter pilot Graeme Gale has described the race against darkness to rescue Mr Bowers from the ship.
"It was late in the evening, so we were always going to be fighting daylight," he told Radio New Zealand today.
"It's not the type of place that you want to go out to do a winch off a boat when it's a dark, so it was pretty important to get out there in a hurry."
Mr Gale said there was quite a big swell and the ship was "heaving and rolling" when the helicopter arrived.
"When I first got there they had the patient in midship, which was impossible to winch off - there was that many tables and winch arms and fishing equipment that you would get snagged on.
"If you got snagged in the middle of a winch, it would literally pull you out of the air, so he had to be repositioned up to the bow of the ship."
The helicopter crew winched an intensive care paramedic onto the ship, who helped to move Mr Bowers to the bow of the ship. He was conscious as he and the paramedic were winched onto the helicopter.
Mr Gale said it was "right on the edge of darkness" by the time the rescue was complete, with night falling only 15 minutes later.
Mr Bowers' mother, Mary, yesterday said her son had a "total, horrible accident" as he was putting on his lifejacket.
"Part of it caught in a belt that was moving, and it tore his shoulder out and mutilated his arm a bit. He's had part of his arm cut off. Horrific."
Mr Bowers' dislocated shoulder had to be put back into place, while his forearm had to be amputated below the elbow.
MPI director-general Martyn Dunne had been in touch with the family and said he was "deeply concerned" by the accidents.
"There will be an investigation into this incident, but right now our focus is on supporting him and his family."
- By Matthew Backhouse of APNZ