He faced Warrnambool Magistrates Court on Wednesday alongside his fellow trainer and former assistant Jarrod McLean.
McLean and stablehand Tyson Kermond have also pleaded guilty to three animal cruelty charges.
Charges initially filed by prosecutors referred to the torture of animals, but lawyers for the trio made it clear they admitted the charge on the grounds of abuse only.
Weir, who is represented by Ian Hill KC, is also pleading guilty to a firearms charge.
McLean has admitted to possession of cocaine.
A number of other charges have been withdrawn.
A pre-sentence hearing is continuing for the men who have all appeared in court in person.