The James Bond actor is taking over after The King's Speech star quit last month, admitting that he was having trouble finding the voice of the Peruvian bear.
Whishaw, 33, told the Daily Mail he was asked to audition for director Paul King's film "quite out of the blue" and was initially unsure about the project.
"I resisted a little bit, because I had a bad experience doing this kind of work in the past and I thought I was no good at it. But I was persuaded to go, slightly grudgingly," he said.
The film, due out in November, also features Nicole Kidman, Peter Capaldi, Hugh Bonneville, and Julie Walters.