The course would start and finish at the Fuji Speedway circuit at the base of the mountain, they said in a joint statement.
"The combination of the stunning scenery of the Mount Fuji region and the stern challenge that the Olympic and Paralympic courses will deliver a fantastic spectacle for cycling fans in Japan and across the world."
The course length is approximately 22.1km, with an elevation gain of approximately 423m. The men will complete two laps during their time trial while the women will do one.
(With inputs from agencies.)