The author previously revealed that he is a fan of the show but added that it isn't science fiction.
Pratchett has now explained his criticisms of the series in an interview with Sky.
"I keep thinking I ought to dislike Doctor Who," he said. "Because it's made of 'makeitupasyougoalongeum' and he has a screwdriver that can repair marriages, launch boats."
He continued: "I think there was an episode where the Tardis towed planet Earth. What I liked was the teacups were rattling. If the teacups are rattling, how high is the tsunami in the Pacific at this point?"
However, Pratchett explained that he does enjoy watching the programme.
"It's hugely gripping entertainment," he said. "But it's totally pants science fiction. Because there really isn't any science."
An adaptation of Pratchett's novel Going Postal begins on May 30 at 6pm on Sky1.