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The man, who was in his 40s, left Whangarei two days ago and fished at the Mokohinau Islands.
His wife notified emergency services when he failed to return on Saturday.
Police said the man's boat was spotted by a Coastguard plane that went to search for him early on Sunday morning.
A spokeswoman said a boat later reached the man's vessel, which was anchored at The Needles, and found him dead on board.
She said it appeared that he had died from a medical event.
A police launch had been sent to recover the body and the Coroner informed.