Michael Whitaker and Portofino. © Remco Veurink/FEI
Whitaker's stallion, Tackeray, tested positive to traces of altrenogest, a synthetic hormone. It is found in the product Regumate, which can be given legally to mares. It is used to modify estrous-related behaviours that interfere with performance.
Whitaker, a silver medalist at the 1984 Olympics and a four-time Olympian, has requested a B sample and a hearing before the FEI's tribunal.
Whitaker withdrew from the Global Champions Tour competition in Monte Carlo on Friday, following a preliminary hearing, and also missed the Hickstead Derby in Britain at the weekend.
A ban on Whitaker would mean he will miss the European Championships in August.
Whitaker has reportedly said that there was a mix-up with a feed that was meant for his top mare, Portofino.
Equestrian sport has been plagued with doping allegations recently, across several discplines. Two endurance riding members of FEI president Princess Haya's family are under investigation; last month the German Equestrian Federation disbanded its top-level teams after doping allegations; and last week dressage rider Isabell Werth was also suspended. At the Olympics last year six riders were suspended following positive tests.