Conte is accused of failing to report alleged match-fixing involving Siena when he managed them in the 2010-11 Serie B season and is facing a long ban from football after a plea deal was rejected on Wednesday.
In a statement on the club's official website, Agnelli said: "The decision taken yesterday by the FIGC's national disciplinary committee, which opposed a plea bargain that had already been considered and approved by the federal prosecutor, is testimony to the complete inadequacy of the sporting justice system and the Federation within which it operates.
"Once again, I detect an inability to interpret the requirements of today's top-level professional game.
"Having chosen to make a plea bargain in order to limit the damage of an antiquated and contradictory system of sporting justice, one is confronted with a dictatorial system that deprives the club and its employees of any right to defend themselves and their honour.
"It is the respectability of individuals that is being put in danger and therefore it is up to them to have the final say on the decisions to be made, in the knowledge that Juventus will support them at every level of the judicial system."