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