Godolphin trainer Mahmood Al Zarooni faces the loss of his licence after admitting to treating horses in his care at Newmarket with anabolic steroids in a major embarrassment for Sheikh Mohammed's operation.
The trainer will front a British Horseracing Authority (BHA) disciplinary panel hearing after samples taken from 11 horses in his care at Newmarket were found to contain banned substances.
Al Zarooni has trained a host of big-race winners since joining Sheikh Mohammed's operation and told the Godolphin website he had made a "catastrophic error".
"I deeply regret what has happened. I have made a catastrophic error," Al Zarooni said on www.godolphin.com.
"Because the horses involved were not racing at the time, I did not realise that what I was doing was in breach of the rules of racing. I can only apologise for the damage this will cause to Godolphin and to racing generally."
Godolphin racing manager Simon Crisford said the Godolpin operation was in shock.
"This is a dark day for Godolphin. We are all shocked by what has happened," he said.
"His Highness Sheikh Mohammed was absolutely appalled when he was told and this is completely unacceptable to him. We will await the outcome of the BHA inquiry before taking any further internal action.
"Sheikh Mohammed has instructed me to begin an urgent review of all of our procedures and controls. That is already under way and we will take advice from the BHA in completing it."
Godolphin said no further comment would be made pending the completion of the BHA investigation and inquiry.
A statement on the Godolphin website said leading 1000 Guineas contender Certify would not be allowed to run in the Group One race next month.
"Following an inspection of Zarooni's stable by officials from the BHA, traces of prohibited substances were discovered in a number of the horses tested, including Certify," the statement said.
"The BHA has advised that, as a result, the filly will not be allowed to take part in the Qipco 1000 Guineas at Newmarket next month.
"Al Zarooni has admitted that he was responsible for the administration of the prohibited substances."
The BHA said that on April 9 this year samples were obtained from 45 horses trained by Al Zarooni and on Monday afternoon it had received written advice from the Horseracing Forensic Laboratory 11 of the samples contained the prohibited substances ethylestranol and stanozolol.
Certify, unbeaten in four career outings and winner of the Shadwell Stud Fillies' Mile at Newmarket in September, was one of the seven horses whose sample tested positive for ethylestranol.
Gold Cup runner-up Opinion Poll was one of four horses which tested for stanozolol,
Ethylestranol and stanozolol are prohibited under the British Rules of Racing at any time - either in training or racing.
The BHA has barred the horses in question from racing for an indefinite time.
A date for the hearing has yet to be announced.