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Rescue Coordination Centre New Zealand, which had been co-ordinating the search since 6.15 am today, said he was found 166km east of Norfolk Island at 11.50am.
Search and Rescue Mission Coordinator Dave Wilson said the centre responded when a distress beacon from the yacht Waimanu was activated.
It was not yet known what happened to his yacht, Waimanu.
A commercial vessel, the Norfolk Guardian, has just picked him up, according to Maritime New Zealand. The ship is due to arrive in Norfolk Island at 11.30pm tonight.
A New Zealand Defence Force C-130 Hercules aircraft was sent to the location of the beacon, and the Norfolk Guardian was diverted to the location.
"The yachtsman is moving and seems unharmed but has not been able to radio the C-130," Wilson said.
"He was sailing single-handed from Vanuatu to Marsden Point."
Waimanu is a 10 metre sloop and it is not yet known what had happened.
"There is a strong 30 knot southerly wind blowing at the location of the life-raft, and the sea is rough with three metre swells," Wilson said.
This morning, the Hercules aircraft was deployed from Auckland.
Air Commodore Darryn Webb earlier said the yacht activated its emergency beacon early this morning.
The Hercules aircraft spotted the skipper of SV Waimanu waving from a life raft a few minutes after reaching the yacht's reported location.
"The crew has yet to establish communications with the skipper but he is moving around in the life raft and waving at our aircraft," Webb said.
"We are pleased to be able to help."
A survival pack with water, food and a note has been dropped to the yachtsman.
The 10-metre yacht, which is equipped with a life raft and a handheld VHF radio, was sailing from Vanuatu to Marsden Point on the east coast of Northland.
The Hercules will remain overhead the life raft to monitor the rescue effort.
Norfolk Island is about 1000km north of New Zealand.