Stewards issued the charges after police raided Weir's stables near Ballarat and Warrnambool on Wednesday as part of an investigation into allegations relating to the corruption of betting outcomes and animal cruelty.
Darren Weir and two of his horse training associates have been slapped with several charges by Racing Victoria.
Trainer Jarrod McLean, 38, and licensed foreperson Tyson Kermond, 26, were quizzed at Racing Victoria's offices yesterday.
Racenet will provide an update once the show cause hearing concludes on Friday evening.
Victorian trainer Tom Dabernig said Prince Of Penzance's Cup success should be looked at.
The Coalition for the Protection of Race Horses also expressed concerns.
A jigger is usually a small electrical device used in conjunction with a whip to stimulate a horse to run faster.
Racing authorities in New South Wales yesterday demanded Weir show cause why horses trained by him should be allowed to race in that state.
On Wednesday, police seized a firearm, a substance believed to be cocaine, and four illegal Taser-type devices at the Melbourne Cup-winner's stables.
"The core responsibility of Racing Victoria is to protect the integrity of the sport and to enforce the Australian Rules of Racing, ensuring both a level playing field for all and the health and welfare of horses competing in Victorian races", Thompson said.
Weir is now the most successful horse trainer in Australia.
Police seized "jiggers" from the 48-year-old Melbourne Cup winning trainer's stables with allegations of animal cruelty and corrupt betting practices being investigated.
Weir is Australia's most successful trainer and prepared 2015 Melbourne Cup victor Prince of Penzance, ridden by Michelle Payne. Since then, he has taken his total of Group One wins to 36, with the highlight being Prince Of Penzance's historic victory, when Payne became the first female jockey to win Australia's most famous race.
A five-time Melbourne premiership victor, Weir runs the biggest stable in the country with more than 600 horses on the books and dozens of staff at both locations.