Eleven horses tested positive for steroids, including stanozolol - the steroid used by disgraced Olympic sprinter Ben Johnson at the Seoul Olympics.
The trainer, Mahmood Al Zarooni, is to attend a British Horseracing Authority disciplinary inquiry after the positive tests from horses in his care at Newmarket, southern England.
"I deeply regret what has happened. I have made a catastrophic error," Al Zarooni said on Godolphin's website.
"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."
The BBC reports that the 11 horses have won over £1.3 million in prize money in their careers and one is Certify, who is unbeaten in four races and will now be prevented from running in the 1,000 Guineas at Newmarket in May.
Godolphin racing manager Simon Crisford said the discovery marked a "dark day" for Godolphin.
"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 underway and we will take advice from the BHA in completing it."
- Sports & Recreation
- Mahmood Al Zarooni