Firth exited the live-action/CGI hybrid project in June, though it was an amicable departure. Producer David Heyman told the Daily Mail, which broke the news, that the Oscar winner's voice was ultimately "too mature" for the character.
Paul King is directing "Paddington," which remains on track for a Christmas Day release in the U.S.
Heyman and King have been searching for a "slightly more open and younger voice" for the optimistic bear, who arrives in England from Peru with a sense of wonder.
Whishaw has been in London recording Paddington's dialogue at a post-production facility.
"He breathes and he speaks and he sounds like Paddington, rather than the most beautiful chocolate-voiced man [Firth] on the planet," King told the Daily Mail.
"Paddington" co-stars Nicole Kidman, Hugh Bonneville, Sally Hawkins, Julie Walters and Peter Capaldi.
Whishaw did not grow up a fan of the beloved character and even doubted whether he was up to the challenge of filling Firth's shoes, revealing to the Daily Mail that he "had a bad experience doing this kind of work in the past, and I thought I was no good at it." However, Whishaw also has a young niece and is excited to contribute to a movie that is expected to delight children of all ages.