Zawraq will miss the Investec Derby at Epsom on Saturday.
Dermot Weld's colt has not fully recovered from a minor setback he suffered earlier in the week and will play no part in the premier Classic.
Angus Gold, racing manager for owner Sheikh Hamdan Al Maktoum, said: "It's bad news.
"He did a bit of work this morning and moved beautifully under Pat Smullen, but by the time he got back to the yard he was definitely not right again.
"It's very bad timing."
Zawraq had been prominent in the ante-post betting lists for the Derby after convincingly winning his two starts to date.
But after completing a satisfactory piece of work on Tuesday morning, he was found to have been slightly lame upon his return to the yard.
Initial X-rays and scans suggested the injury was not serious, with hopes high in the Weld camp he would prove his fitness in time for Epsom.
Zawraq engaged in promising light exercise on Wednesday, further fuelling the optimism, but connections were forced to draw stumps after the horse cantered on Thursday morning.
Gold said: "He (Smullen) said that when Zawraq flexed one of his joints he was a bit sore.
"Maybe it is something do with a joint that did not show up on the scans or X-rays.
"Hopefully it's nothing too serious, but we can't think about future plans until we get to the bottom of what is troubling him."