A fisherman has been rescued from the Manukau Harbour barely alive after spending five hours in choppy seas after his dinghy was swamped.

The Northern Coastguard said the 34-year-old man was suffering from severe hypothermia and drifting in and out of consciousness when he was spotted in the middle of the Purakau Channel at just before 4am.

He had earlier rowed out from Green Bay to set fishing nets at 10pm when his 2m wooden dingy overturned in waves.

The man was reported missing just before midnight.

Three Coastguard rescue vessels and the police rescue helicopter started searching for the man.

After nearly four hours of searching in choppy conditions across the entire Manukau Harbour the man was found.

His overturned dinghy was close by.

He was wearing a wetsuit and lifejackets which his rescuers credit for keeping him alive.

He was rushed to a waiting ambulance ashore at Mangere Bridge.

"He's a very lucky man," said Rod Frost who was the skipper of the volunteer Papakura coastguard crew who located the man.

"There were some rough conditions out in the Manuaku Harbour, and although we were searching much of the night, we only spotted the man when our searchlights picked up the reflective strips on his lifejacket."

"The lifejacket the man was wearing kept him afloat throughout the night, and that undoubtedly saved his life."

However the man was unprepared with only oars and a lifejacket and no forms of communication to signal if he got in trouble.

Coastguard urged boaties heading out on the water to wear a lifejacket, carry at least two forms of waterproof communication, and file a trip report with Coastguard to aid search and rescue teams if they needed to look for a missing craft.

- NZ Herald