Sir Geoffrey Shakerley, who took the photographs at Saturday's wedding, admitted replacing the figure of Prince William in the shot released to the press, with a shot from a different frame.
"Prince Edward said he didn't think Prince William looked absolutely his best, so digitally we were able to put in another picture from one of the other shots where he is smiling and laughing," he said.
Sir Geoffrey also revealed that a new "alternative" official photograph of the wedding couple is to be released, showing them against a "cleaner background" than the cabinet originally behind them.
The moves were condemned by Horst Faas, European photo editor of the Associated Press news agency and a legendary photo-journalist. He said it was a "terrible precedent".
He said: "How can we trust the official hand-out photographs from the Palace if something like this is happening? To change a picture is against the very basic rules of photojournalism. All our editors are permitted to do is improve the quality by cropping or removing specks of dust. You can't make the sky blue when it was a grey, rainy day. A photo is a photo, is a photo and you shouldn't tamper with it."
But Sir Geoffrey said last night: "I'm sure Prince William would like the best picture of himself. I hope I haven't in any way erred. I feel very strongly that poor Prince William has a hard enough time as it is so I don't want to bring him into the picture by doing this."
Sir Geoffrey was backed by Robert Simpson, his assistant: "Everybody, including Prince William, was in a very happy and jubilant mood throughout the day and when the official formal family photographs were taken. However, Prince William had been caught at that particular moment glancing down and away from the camera.
"Even though it is not a matter of course to digitally manipulate photographs and transpose one head for another, it was a spur-of-the-moment decision by Sir Geoffrey to do so, in order to show Prince William in the best light." The original of the doctored photograph has not been released, but others in the same sequence show the Prince looking glum.
New technology makes it easy for the entire meanings of photographs to be changed. The London Evening Standard apologised to John Prescott, the Deputy Prime Minister, for replacing a bottle of beer with a bottle of champagne to try to give the impression he was a champagne socialist.