Melbourne Cup-winning trainer Gai Waterhousefaces a likely fine of some thousands of dollars after being charged by stewards over the raceday treatment of one of her runners in Tuesday's big race.

Waterhouse and Mikel Delzangles, trainer of 2011 Cup winner Dunaden, were quizzed by Racing Victoria stewards hours before the Cup after security guards witnessed handlers giving medication to their horses.

Dunaden received an oral treatment for an ulcer, while the Waterhouse-trained Tres Blue was given a cream for an irritated hoof.

The treating of horses on race day is not permitted, and the Australian Racing Board has introduced a mandatory six-month ban for the offence.

Both trainers will face the Racing Appeals and Disciplinary Board on Friday afternoon.