It is understood the set-up was a prototype a friend had made for him.
Fortunately the paddler, who is not currently a member of an official waka ama club, was equipped with a life jacket and a cellphone in a waterproof bag.
Senior Sergeant Pat Davis said the man phoned his partner who raised the alarm with police about 7pm.
Coincidentally the crew of a Royal New Zealand Air Force P-3K2 Orion were conducting a training flight off the coast west of Auckland, and were alerted to the mayday call.
Police had issued the mayday, concerned about the man's safety and the Orion crew quickly diverted to the scene, arriving there within 10 minutes.
From the air the crew located the man in the water using the aircraft's infrared sensors and relayed the man's exact position through to maritime radio.
A local was dispatched in a boat and the paddler used the light on his phone to guide the rescuers to his location in the water.
Davis said the man was not injured and he and his damaged waka were safely delivered to shore.
The Orion remained in the area until the man was safely out of the water.
Ngaro Tumai, a club representative with Te Tai Tokerau Polynesian Canoe Association - the regional body for the 11 waka ama clubs in Northland - said the rescue served as a stark reminder to those in the sport to ensure their waka were seaworthy given the break away from the water due to lockdown.
Tumai said Northland clubs had notified their members that all club waka, including six-man, double and single waka, were grounded during lockdown and level 3.
If members chose to use their own single waka, which was allowed, they should obey the level 3 regulations.
He said it was fortunate the paddler involved had been wearing a life jacket and had a phone to call for help but the timing of the harbour trip could have been better.
"It would have been pitch black when he fell in. I definitely wouldn't advise going out in the dark and definitely not alone," Tumai said.