They had launched from Te Paki stream earlier in the day to go fishing on the west coast.
Police were contacted by the Maritime Operations centre in Wellington, who were in contact with the duo.
Mr Metcalfe said the men were told they could be winched off the boat by helicopter but they made it clear they would not be leaving the vessel.
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.
"There are no other rescue options available in that area. The nearest coastguard is based at Opononi," Mr Metcalfe said.
They wanted to be towed but there were no other boats nearby.
It didn't take long before the helicopter crew spotted the boat, still at anchor, with only its bow above 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 climb a cliff at Te Waiawa Bay."
The helicopter crew spoke with the men, who were uninjured. Police were today trying to track down the 41-year-old from Whangarei and his 32-year-old friend from Kaitaia.
"They are very, very lucky to be alive, Mr Metcalfe said."
