An 73-year-old man who fell off the back of his commercial fishing boat in Whangaroa Harbour is believed to have spent six hours in the water before he was rescued.

The Northland Rescue Helicopter team got the call for help not long after the man was discovered in the water at Waihi Bay, near Totara North about 5.40am yesterday.

In the darkness the pilots used night vision goggles and navigated by the aircraft instruments to make it through the cloudy and rainy conditions from their Whangārei base to the harbour.

The crew arrived at daybreak which coincided with a window of opportunity to carry out the rescue as the blustery conditions cleared.

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"It was quite a tricky situation in the bay with a person in the water," a spokesman for the helicopter team said.

St John intensive care paramedic Scott Mears, who was the winch operator on board the rescue helicopter, said the wind and rain made it challenging.

"A member of public, who was on a dinghy, was able to locate the patient in the water and hold them out of the water until help arrived," Mears said.

The helicopter crew located the dinghy and winched the patient out of the water.

The man was flown to Whangārei Hospital unconscious and in a critical condition. However, late yesterday he was making progress and was reported to be in a stable condition with family at his bedside.

Mangonui Police Constable Brett Walford said the fisherman fell off the back of his boat which had been moored at Waihi Bay for three days.

He was unable to get himself back on to the boat and could only yell for help while he floated in the cold water, rain and wind.

Walford said a local eventually heard the man's cries for help early this morning. He went out in his dinghy but was unable to get the man into his boat or back on the commercial vessel. So he took a life ring from the larger boat and put it around the fisherman in the water.

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He also rang 111 and the rescue helicopter crew winched the man to safety about 7.50am yesterday.

"While the sea was calm, it was pouring with rain," Walford said.

A Coastguard Whangaroa Rescue vessel was also called out to help search about 7am and checked with other vessels in the area to see if anyone else was missing off the fishing vessel. They were stood down once the man had been rescued.