Corine Barande-Barbe has made a formal complaint to the French police after it emerged late on Sunday night that Cirrus Des Aigles had tested positive for a "massive" amount of a banned substance.
France Galop, the governing body of the sport in France, discovered a high amount of an anti-inflammatory drug in a routine test that was carried out after the Dubai Sheema Classic victor finished second in the Prix d'Ispahan at Longchamp, in Paris, last month.
Cirrus Des Aigles, trained by Barande-Barbe, who is French, was fancied to win the Group 1 contest but had to give way to Golden Lilac.
"In Dubai, Hong Kong or England only the people connected with the horse can go into the stables whereas in France it seems anyone can go in," Barande-Barbe said.
"We are very scared that something has happened - someone could have killed the horse.
"We have made a formal complaint to the police in France and they will be making an inquiry."
France Galop are in no doubt that the sample is from the three-time Group 1 winner but are investigating the horse's medical records and the possibility of malpractice at the Longchamp racecourse.
According to Barande-Barbe, the level found in Cirrus des Aigles was similar to that given to horses that have suffered serious injury, such as a broken leg. "There was so much substance in the test result that it must have been done on purpose - no horse person would administer such an amount," she said.
The France Galop inquiry could take up to two weeks, but is likely to be completed by the end of the week.
If found guilty the 54-year-old Chantilly handler could be suspended, or even have her licence, which she has held since 1991, revoked.