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Otago Coastal Surf Life Saving search and rescue team members pulled the man out of the water and into an inflatable rescue boat about 150m from the shore, police search and rescue leader Matt Sheat said.
St John transported the victim to Dunedin Hospital with suspected hypothermia, Const Sheat said.
He was conscious and talking.
The man had been in the water about 45 minutes before he was rescued about noon.
A police spokeswoman said police were notified of the incident at 11.24am when police officers were alerted to a water rescue off Brighton Rd at Ocean View, involving a sea kayaker.
The man was reported to be in the water with a life jacket, holding on to the side of his kayak about 300m to 500m from shore, she said.
A beach-goer said she was walking her dog when she saw a man in a kayak who appeared to be separated from two of his friends who were coming in towards the beach.
When she returned from walking the dog, the man had drifted further out from the shore before help arrived.