Melbourne Cup-winning trainer Darren Weir has been charged with animal cruelty, conspiracy and weapons offences.

The banned horse trainer was charged by Victoria police on Wednesday, after officers raided his properties at Ballarat and Warrnambool in January, which uncovered a a gun and conductive energy devices, known as jiggers.

Weir is one of four men charged over the investigation.

He is up on nine charges: conspiracy to defraud Racing Victoria stewards, three counts of engaging in torturing, abusing, overworking and terrifying a thoroughbred racehorse, three counts of causing unreasonable pain or suffering to a thoroughbred racehorse, possessing an unregistered gun and using a controlled weapon without an excuse.

A 38-year-old Yangery man is facing 16 charges including conduct that corrupts betting outcomes, animal cruelty and possessing cocaine.

A Warrnambool man, 27, has been charged with six animal cruelty offences and one count of conspiracy to defraud Racing Victoria.

A 31-year-old Warrnambool man has also been charged.

All four are due to appear at Melbourne magistrates court on 23 October.