Isabell Werth and Whisper at the 2009 CDI Wiesbaden, where the combination won both the Prix St Georges and Intermediare I.
Germany's Equestrian Federation said in a statement that the FEI had suspended Werth from all competitions.
The test was carried out in the same week that Germany's equestrian team was disbanded because of doping allegations. The ongoing saga of doping allegations have plagued Germany since the Olympic Games.
Whisper (Wolkentanz I / Einstand), a 10-year old Hanoverian gelding, tested positive to the substance Fluphenazine in routine testing on 30 May at the 2009 CDI international tournament in Wiesbaden. Werth and Whisper won both the Prix St Georges and Intermediare I events at the competition.
"This is a disaster for equestrian sport, but we will not let ourselves be discouraged by the bad news and will continue along the road for fair equestrian sport," German federation president Breido zu Rantzau said.
A hearing is to be held today by the FEI to decide whether to uphold the suspension. The Federation said that Werth would request the opening of the B sample.
Werth, 39, won team Olympic gold medals in 1992, 1996, 2000 and 2008, and the individual gold in Atlanta in 1996.
Fluphenazine is a sedative, and part of a group of drugs known as neuroleptics. In humans, it is used as an antipsychotic drug for the treatment of psychoses such as schizophrenia and bipolar disorder. Fluphenazine has a history of unlabeled use in horses. Neuroleptics differ from other sedatives in that patients are easily arousable and will respond when stimulated. Neuroleptics suppress spontaneous motor activity, conditioned avoidance, and aggressive behaviour.