The ad, created by DDB London, features Paddington replacing his trademark marmalade sandwich with ones containing Marmite and cheese and finding it "really rather good", as part of Marmite's long-running "love it or hate it" campaign.
In a letter to The Times, Bond quashed the rumour that he was responsible for writing the ad and said: "I have to report that although Paddington found the sandwich interesting, bears are creatures of habit. It would require a good deal more than the combined current withdrawal of Northern Rock to wean him off marmalade, if then."
Bond added that he was not consulted about the ad and feels that it was a mistake. He said: "Now there's no going back".
Many fans have been outraged by the Marmite ad, seeing it is a betrayal of Paddington's true character and at least 18 Facebook groups have already sprung up, including "Love it or Hate it", "Paddington eats marmalade, Not Marmite" and "We don't appreciate Paddington eating Marmite".
Karen Jankel, Bond's daughter and managing director of Paddington & Company, agreed to the proposal from the Copyrights Group, Paddington's licensing agents, despite strong reservations, because she believed it would lift the bear's profile and bring him back to British TV.
Tribal DDB said that Bond was aware of the campaign's development and issued this statement: "We have been amazed at the overwhelmingly positive reaction to our campaign and in the true spirit of love it or hate it, it's also great to see those who prefer to see Paddington eating marmalade entering into the debate."
The ad campaign comes as Paddington Bear books also set to be adapted for the big screen in the hands of David Heyman, the producer of the Harry Potter films.
Heyman said that Paddington Bear is a "universally loved character and I have wanted to bring him to the big screen for some years". He added that Paddington's story was essentially that of an immigrant arriving in London and trying to find a home and family.