The stewards have decided to charge Waterhouse after security guards reported to authorities that horse Tres Blue received medical treatment against racing rules on Tuesday morning.
The Australian Racing Board has introduced a mandatory six-month ban for the offence of treating horses on race day.
A media release from Racing Victoria said: "Racing Victoria Stewards this afternoon laid a charge against licensed trainer Mrs Gai Waterhouse under AR 178E(1) which states:
"'Notwithstanding the provisions of AR 178C(2), no persons without the permission of the Stewards may administer or cause to be administered any medication to a horse on race day prior to such horse running in a race'.
"The particulars of the charge are as follows:
"On 5 November 2013, Tres Blue, was entered in race 7, the Emirates Melbourne Cup (Group 1) over 3200m at Flemington.
"On the morning of 5 November without the permission of the Stewards, a stablehand employed by Mrs Waterhouse administered flamazine, a medication, to Tres Blue."
The Racing Appeals and Disciplinary Board will hear the charge against Waterhouse at 1pm on Friday.
Waterhouse has denied there was anything sinister involved in the treatment. She says she is also appealing the decision to the Racing Appeals Tribunal.
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