The Taupo Greenlea Rescue Helicopter was notified of the beacon signal by RCC at about 5pm.
The man was in the water for about 3 hours before he was picked up in the upper reaches of the river.
"They were picked up and flown back to a farm house where they received some good old Kiwi hospitality.
"They weren't injured but they were wet and cold.
"Unfortunately in the course of the incident both of them have lost their kayaks and some of their personal belongings which were in the kayaks."
A LandSAR team assisted in the rescue, Mr Rendall said.
The rescue helicopter said the boulder the man was stranded on was in the middle of a "swiftly flowing series of rapids" in the river.
The LandSAR team were able to set a rope anchor and pull the man to safety, it said.