Emergency services were called to an area off Auckland's Cornwallis wharf shortly after 3pm today.
The Police Eagle helicopter was among those called to the rescue.
One of the kayakers had managed to get back onto the vessel, but the other remained in the water.
The Eagle helicopter remained in view of the pair.
"Our crew kept an eye on them and reported back to the Police Maritime Unit and Coastguard as well as their location and condition,'' a statement said.
"The Coastguard and Westpac Rescue Helicopter were also deployed but officers on board the Eagle soon noticed one of the kayaker's condition deteriorating.
"The guy who was still in the water had started to turn blue and was struggling to hold on to the kayak, so one of our rescue swimmers was sent into the water."
