An extensive search and rescue operation ran for three hours on the Whangarei Harbour before the man at the centre of the search alerted rescuers he was safe on land.

Northern Region Coastguard spokeswoman Georgie Smith said there were fears for possible people in the water after a 12ft runabout went past boats in the Marsden Cove area without a skipper or passengers around 5.30pm on Tuesday before hitting another vessel's wake and flipping.

People aboard a boat reported the incident and told emergency services they could not see anyone on board when the vessel capsized.

Ms Smith said an aerial and sea search including a fixed-wing plane from Kerikeri was launched in the Marsden Cove area.

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Coastguard crews from Tutukaka and Whangarei were also deployed and began searching along with a team from nearby Ruakaka Surf Club.

At the time Coastguard issued an urgent plea for information about the driverless vessel or its owners.

But it wasn't until three hours after the alarm was raised that the man, who had started his boat about 20m off shore then fell out, realised all the activity on the harbour may have been in relation to his missing boat that he contacted authorities.

Ms Smith said it served as a reminder to boaties that if they were involved in something unusual on the water, and particularly when they became separated from their vessels, to contact Coastguard and police and let them know the situation.

"We were delighted he was safe on shore. We take these calls seriously and respond immediately so if there is an incident and people are safe please call us."