The film, starring Robert Carlyle, received 11 nominations including best film, best original screenplay and best actor. Mrs Brown, starring Dame Judi Dench and Billy Connolly, was nominated eight times, but Bean: the Ultimate Disaster Movie - the second most successful British film made - was ignored by the judges.
Despite being largely panned by the critics, Bean, featuring the bumbling nerd created by Rowan Atkinson, grossed more than $218m world-wide and has still to be released in Japan. Only Four Weddings and A Funeral was more successful, taking $225m. The Full Monty has so far made $203m.
Peter Bennett-Jones, Rowan Atkinson's agent, said he was not surprised by the nominations. "We are all very proud of the film we have made and I was slightly irritated that Bean did not receive any nominations at all because it was a very successful film, but that is just indicative of the attitude.
"There is a preconception that a film like that will be rubbish and there is a certain amount of prejudice against big broad comedies, but it was a good piece of work and we are were very happy with it," he said.
Caroline Westbrook, reviews editor of Empire magazine, said that Baftas tended to concentrate on critical acclaim.
"Bean did extremely well but it was not recognised for its screenplay or fine acting so you would not expect it to be nominated," she said. "It was fine for what it was, but you should not equate box-office clout with awards-worthy films."
Despite the lack of nominations for Bean, British films have received widespread recognition this year, but The Full Monty will face stiff competition in the best film category against LA Confidential, Mrs Brown and the current box-office hit Titanic, which received five nominations including best direction and visual effects.
The film, tracing the fortunes of a group of British steelworkers who turn to stripping after their attempts to find employment fail, has also been nominated for the best original screenplay where it is competing against Boogie Nights, Mrs Brown and Nil by Mouth.
Helena Bonham Carter, Kathy Burke and Dame Judi took three of the four nominations for best actress and Robert Carlyle, Billy Connolly and Ray Winstone are all nominated for best actor. Kevin Spacey and Kim Basinger were also both nominated for their performances in LA Confidential.
This year in a move to recognise the growing importance of British talent on the world stage, Bafta has created the first British Academy Film Awards which concentrate solely on films. The list of nominees for television will be announced at a later date.
Lord Puttnam, vice-president of the British Academy of Film and Television Arts, said: "For the first time in years there is a real sense of vibrancy and excitement around the British film industry. The creation of this award could not be more timely."
Tim Angel, the chairman of Bafta, said: "British films are enjoying a renaissance and the awards will contribute to this climate of confidence and optimism.
"They should reflect the UK's position as a leading film-making nation on a world stage."
The winners will be announced on 19 April.