The great Brit, who plays spy chief M in the film, was surprised to learn that Sam Mendes was not recognised in the Best Director category and that her co-stars, 007 Daniel Craig and movie villain Javier Bardem, had been overlooked in the top acting nods.
She tells the Bbc, "I'm very, very sorry that nothing has been recognised. That's a great pity. I thought Sam Mendes directed it absolutely beautifully. It was a terrific film."
And Dench only hopes the Bond films haven't been deliberately shut out in the main categories over the years because of their commercial success.
When asked if she thought there was a bias against the superspy franchise, she adds, "There may be. I don't know. I hope not. I just think that all round it was really wonderfully directed and presented and filmed and lit and shot."
Skyfall didn't get left out completely - Adele's theme tune landed a nod for Best Song, while the film also scored well with technical nominations for production, cinematography, sound editing and mixing.
The action-packed movie fared better with bosses at the British Academy of Film and Television Arts (BAFTA) Film Awards, securing nominations for Dench (Supporting Actress) and Bardem (Supporting Actor), while it was also mentioned in categories for Original Music, Cinematography, Editing, Production Design, Sound and Outstanding British Film. The nominations top a stellar year for 007 after Skyfall became the first ever Bond movie to break the billion dollar mark at the global box office.