The Qualifications and Curriculum Authority is consulting on whether to set up a GCSE and A-level in the subject separate from existing English-language exams.
The qualification, endorsed by poet laureate Andrew Motion, would be modelled on creative writing courses in universities.
But at a conference of writers, academics and teachers this week, Mr Pullman, author of the His Dark Materials trilogy, condemned the idea. "I'm dead against it," he said. "It would inevitably fall into the hands of bureaucrats, and be taught willy-nilly by people who only know how to follow instruction booklets.
"In the real world, literary work is judged by whether it sells copies or lasts 100 years. But you can't judge GCSEs that way. It's using callipers to measure the density of fog. Flood them, saturate them, suffuse them with the spoken word.
"If pupils see you as a purveyor of stories, you'll be able to keep them quiet in the classroom. The effect is pervasive."
Plans for the new qualification are in their infancy, but by 2015 the QCA hopes that every secondary pupil will work with a poet or novelist, learn five favourite poems by heart, and have their writing published or displayed.
Janet White, QCA English subject officer, said exposure to stories was best achieved by their incorporation into the curriculum.
She told the conference: "Every child should read 50 books a year, minimum.
"How do you know what voice you can try unless you've had an apprenticeship in speaking and learning in a new way?"