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Weir, who was handed a four-year global ban in February for the illegal possession of "jiggers" used to deliver electric shocks to horses, was among four men charged by Victoria State's Sporting Integrity Intelligence Unit, which raided his properties in January.
Police, in a statement on Wednesday, did not identify Weir, 49, but media has widely reported his involvement in the case.
Police said a 49-year-old Australian was facing nine charges including three counts of "engaging in the torturing, abusing, overworking and terrifying a thoroughbred race horse" and three counts of "causing unreasonable pain or suffering to a thoroughbred race horse".
Weir, who trained 2015 Melbourne Cup winner Prince of Penzance, was also charged with conspiracy to defraud stewards of the state racing authority, possessing an unregistered Category A firearm and using the controlled weapon without excuse. Police did not elaborate.
All four men are due to appear at the Melbourne Magistrates' Court on Oct. 23