The marine operations centre lost communications with the boaties about 2.45pm.
The Northland Electricity rescue helicopter, based in Whangarei, was sent to the Far North and began searching the area about 3.40pm.
It didn't take long before the helicopter crew spotted the boat, still at anchor, with only it's bow showing above the water.
"They had been trying to get the motor started when the boat was hit by a big swell and flipped. They managed to swim ashore and and climb a cliff at Te Waiawa Bay," Mr Metcalfe said.
The helicopter landed nearby and crew spoke with the men, who were uninjured.