Runner-up on his Windsor debut before bolting up on his second start at Haydock, the Zoffany colt successfully stepped up to Group Two level with a dominant display at Newbury last month.
Sakheer was all set to test the water in Group One company this weekend, having been supplemented for the Dewhurst earlier this week at a cost of £35,000, but he will not line up on the Rowley Mile.
In a statement posted on Twitter, Varian said: "Unfortunately Sakheer has scoped dirty this morning ahead of his intended run in the Dewhurst Stakes at Newmarket on Saturday.
"This is of course very frustrating and disappointing, and I am very sorry for owners KHK Racing and everyone connected with the horse.
"He will be put away now for the season and we look forward to him returning as a three-year-old."