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The Norwegian sailor is aboard the MV Southern Lily cargo ship, which is due to arrive in Auckland tomorrow.
A dramatic photo released by the New Zealand Defence Force shows the stricken sailor being hoisted up the side of ship by crew using ropes as life rings bob below him in the large swells.
Another crew member hangs precariously from a ladder by one hand while he helps to steady the Norwegian man.
Maritime New Zealand spokesman Vince Cholewa said the MV Southern Lily cargo ship and the Royal New Zealand Air Force Orion arrived on the scene around 5.30pm.
"Conditions are quite rough so it's not straightforward. They've got a line between the yacht and the ship that they're using to transfer the yachtsman."
Cholewa said it was likely the man was transferred from vessel to vessel with a net.
The Lily had originally been expected to meet the sailor around midday, however the ship was held up by heavy seas.
The yachtsman set off a distress beacon after his boat Ilanga was damaged in high winds and heavy seas yesterday afternoon and had been stuck since then.
Earlier this afternoon search and rescue mission co-ordinator Dave Wilson, of the Rescue Coordination Centre, said a southerly wind in the area was blowing at around 55km/h and there is a 5m swell.
Wilson said the sailor was safe on board the damaged Ilanga.
The Royal New Zealand Air Force Orion had left this morning to help with the rescue, but had returned to Auckland due to rough conditions and launched again later in the afternoon.
The 12m-long Ilanga's electrical unit had caught fire and it had started to take on water through a window. The yacht no longer has navigation lights, but before the rescue the skipper had a handheld VHF radio which he turned off at times to time to save power. The yacht has a dinghy.
Air Commodore Darryn Webb said a Royal New Zealand Air Force Orion oversaw today's rescue as the ships crew battled 25 knot winds and 3.5m swells.
It came a day after a Kiwi sailor was rescued 166km east of Norfolk Island.
"We are delighted that we were able to bring good news to the families of the two yachtsmen involved. I'd like to commend our crew and all those involved in these two successful search and rescue operations," Air Commodore Webb said.
Southern Lily captain Shashi Prakash and a Royal New Zealand Air Force squadron were awarded a certificate of achievement in the Search and Rescue Council awards for their rescue in June last year of three people from the boat Platino.
The Platino was damaged in heavy seas 550km off the Northland coast.
One of the five crew of Platino had died after being hit by the yacht's boom. Another was lost overboard.
An RNZAF Orion was in the region and arrived near Platino within 90 minutes of the distress alert.
The Southern Lily was diverted to assist, arriving 14 hours later.