Michael Bond, the 88-year-old author of the books charting the adventures of the marmalade-loving bear, said he was "totally amazed" at any suggestion of sexual content in the film, in which he has a cameo.
"I'd be very upset. I might not sleep well tonight. I can't imagine what the sex references are. It doesn't enter into it with the books, certainly," he told the Daily Mail newspaper.
The British Board of Film Classification (BBFC) has given the film, which opens next week, a "PG" or "Parental Guidance" rating, meaning it may not be suitable for very young children.
It cited "dangerous behaviour", such as when Paddington hides in a fridge in the film, and "mild threat", when a villain threatens to kill and stuff the bear.
The "mild sex references" include a comic sequence where a man flirts with another man disguised as a woman, while the classification also warns of "mild bad language".
However, following a minor media uproar, the BBFC confirmed on Wednesday that it had removed the reference to sexual content on its consumer advice in favour of "innuendo".
Actor Hugh Bonneville, a star of hit TV series "Downton Abbey" who plays a leading role in "Paddington", said the film was "perfectly watchable" for children under eight.
"I saw it with some five-year-olds the other day and the only danger they had was wetting themselves laughing," he told the BBC.
