A statement on the Godolphin website read: "Following an inspection of Zarooni's stable by officials from the British Horseracing Authority, traces of prohibited substances were discovered in a number of the horses tested, including Certify.
"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."
Godolphin trainer Al Zarooni based in Newmarket said on www.godolphin.com: "I deeply regret what has happened. I have made a catastrophic error.
"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."
Racehorse trainer Mahmood Al Zarooni has been disqualified for eight years after 11 of his horses tested positive for anabolic steroids.
The Newmarket Godolphin stables are at the centre of horse doping allegations involving 11 horses and the trainer Mahmood Al Zarooni.