Immediate family had been notified by police.
Organisers also extended their thanks to fellow riders who stopped to provide medical assistance at the scene.
The incident was the second involving a cyclist in the Taupō region today.
A police spokesperson said officers were called to a crash involving a car and a cyclist on Wairau Ave, shortly after 1.30pm.
The cyclist had serious injuries and was taken to Taupō Hospital, he said.
A Taupō Hospital spokeswoman said the patient had since been transferred to Rotorua Hospital in a "stable condition."
Cyclists competing in the Lake Taupō Cycle Challenge are given the option to ride courses ranging from 5 kilometres, to 640 kilometres for the "maxi enduro" race.