Military March, third favourite for the Derby at Epsom on 4 July, will miss the race.
Saeed bin Suroor, who trains the horse for the Godolphin team, said he had suffered a setback.
"We will give him plenty of time and hopefully he will be back racing later in the season," he said.
Military March was a general 6-1 shot for the race behind 5-2 favourite English King and 9-2 chance Kameko.
After two victories at Newmarket last year - including the Autumn Stakes - Military March returned with a promising fourth behind winner Kameko in the 2,000 Guineas earlier this month.