Firth left the production in June, saying he and the producers agreed he wasn't finding the right tone for the polite, yet ever-in-trouble bear from Peru.
"What we needed was a slightly more open, and younger, voice," he said.
Whishaw, who played the gadget-loving Q in Skyfall, said he initially wasn't interested in the gig.
"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.
Paddington, which stars Nicole Kidman, Hugh Bonneville, Sally Hawkins, Julie Waters and Peter Capaldi, is set to be released in late November.
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