Canford Cliffs will miss Saturday's Queen Elizabeth II Stakes at Ascot.
Richard Hannon's star was heading for a mouthwatering rematch with Makfi but didn't scope satisfactorily on Thursday and does not feature among the final declarations.
Hannon told his website,
www.richardhannon.tv: "The scope was marginal, but Canford Cliffs is now such a valuable commodity that you cannot take any chances, so, having listened to veterinary advice from Mike O'Gorman, we have no option but to pull out.
"Everyone in the yard is absolutely gutted, and we realise that it could well cost us the trainer's championship, but the welfare of the horse comes first and you need to be 100% to go into a battle for a Group 1.
"I must stress that the tracheal wash was not terrible, but the reading was disappointing, and, though he'd probably be fine if there was another race coming up in a week or so, the fact is there is nothing left over a mile, just the Foret over seven furlongs.
"However, the great thing is that we have him in training for next year - he has done us proud this season, and he'll be back better than ever as a four-year-old."
William Hill reacted to the news by making Makfi their new 4-5 favourite with defending champion Rip Van Winkle now 11-4 (from 7-2).
Spokeswoman Kate Miller said: '"Racing fans have been denied one of the most mouth-watering rematches of the season with the late withdrawal of Canford Cliffs. Makfi now quite rightly takes the top honours in the betting, with Rip Van Winkle the biggest threat to a French victory."