The classification board warned that "parents should consider whether ... content may upset younger, or more sensitive, children" on films awarded a Parental Guidance (PG) certificate.
A comic sequence in which "a man disguised as a woman is flirted with by another man" was flagged by the censors as containing "mild sex references".
The board also warned: "There are occasional sequences of mild threat when Paddington is chased by the villain who threatens to kill and stuff him, as well as a brief sequence in which Paddington lies unconscious on a table while a taxidermist prepares tools nearby."
Dangerous behaviour which the board considered could be imitated by children included "Paddington hiding from a villain inside a refrigerator and riding on a skateboard while holding on to a bus, as well as a brief scene of a boy strapping fireworks to his shoes".
A single mumbled use of "bloody" also attracted the censors' attention. They advised: "Parents should consider whether the content may upset younger, or more sensitive, children."
Bond, 88, has not yet seen the movie and is said to have not been consulted over the big-screen version, directed by Paul King, although he makes a cameo appearance in it.
He told the Daily Mail when the initial classification warning came out: "I'm totally amazed. 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."
Hugh Bonneville, who plays Mr Brown, told the BBC this week that he thought it "hilarious" that the board had mentioned "mild sex references" in relation to the scene in which he disguises himself as a cleaning woman.
"I was scratching my head thinking 'what are the censors talking about'?" he said.
"There were four- and five-year-olds watching it the other day, laughing uproariously, so I don't think it's going to damage any young children - or indeed any 75-year-olds."
The film stars Bonneville, Peter Capaldi and Nicole Kidman.
Producers brought in Whishaw to replace Colin Firth after The King's Speech star admitted he was having trouble finding Paddington's voice.
Filmgoers have questioned the consistency of the classification board's ratings.
Despite scenes of violence, The Hunger Games: Mockingjay - Part 1, which shows public executions, corpses being devoured by wild animals and the bombing of a hospital, was awarded a 12A certificate, meaning it can be seen by children of any age as long as they are accompanied by an adult.
Recent children's films awarded a Universal certificate include The Lego Movie, Despicable Me 2 and Monsters University. But the hit film Frozen (mild threat) and How To Train Your Dragon 2 (mild violence and threat) were given PG certificates.
Paddington has prompted parodies by web users before its release. A "creepy Paddington" Tumblr has hundreds of images of the loveable bear superimposed on to horror film posters.
- Independent