Having won the 2000 Guineas, the St James's Palace Stakes at Royal Ascot and the Sussex Stakes this season, Bow Echo was being lined up for Sunday's Prix Jacques le Marois.
Announcing the surprise news on his X account, Boughey said: "It is with great disappointment that we have to announce that Bow Echo has had a setback and will be retired from racing.
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"It has been the honour of a lifetime to train a horse like Bow Echo. He has given us some extraordinary days and taken everyone involved on a journey we will never forget.
"To retire unbeaten, having won the 2000 Guineas, St James's Palace Stakes and Sussex Stakes says everything about what an exceptional racehorse he has been.
"Bow Echo's remarkable story began with his owner-breeder, the late Sheikh Mohammed Obaid and it is a great sadness that he was not here to see what a lifetime of breeding was able to produce.
"Bow Echo's unbelievable constitution and extraordinary ability have set him apart. We will all miss seeing him at home and on the racecourse but we are incredibly excited for his next chapter and in time, to see a new generation of his progeny on the racecourse."
