The Richard Mandella-trained colt, who was the 4-1 early favourite for the Derby on Saturday (Sunday AEST) galloped on Wednesday morning without any problem.
That changed by late afternoon when Omaha Beach was found to have an entrapped epiglottis, the cartilage at the base of the airway.
It is generally not a career-threatening problem and is usually corrected with minor surgery.
The role of likely favourite now falls to the Bob Baffert-trained Game Winner, who was the 5-1 second choice.
Omaha Beach's scratching moves Bodexpress into the field with barrier 20.