However, Graham Ashton cautioned it was too early to say if criminal charges would follow Wednesday's raids on properties at Ballarat and Warrnambool where Weir and two other men were arrested.
Officers also seized four taser-like devices, known as “jiggers” in the racing industry, an unregistered firearm and a small amount of what is believed to be cocaine.
“The evidence is supportive at this stage of what we think might have been going on,” Ashton told 3AW on Thursday.
However it was still possible the matter would be referred back to the governing body, Racing Victoria.
Weir, a 38-year-old from Yangery believed to be one of the trainer's foremen, Jarrod McLean, and a 26-year-old were questioned on Wednesday and released by police pending further investigations.
Ashton, who has bred racehorses, said he was confident “overall it's a pretty clean sport” but conceded several scandals had tarnished the industry.
Police believe the jiggers may have been used in combination with other tactics, such as whips, to make horses run faster.
“I'd be pretty alarmed if one of my horses was subjected to that,” Ashton said.
Racing Victoria chief executive Giles Thompson says it is too early to say if Weir, 48, would be suspended from the sport.
“We need to seek legal advice around that; that takes time,” Thompson told ABC News.
“That means that the stewards at the moment are assessing that information, the police are assessing that information and they'll make the next steps when they are comfortable.”
Racing Victoria called in police in August after investigating the allegations itself for some time.
Police say the allegations include obtaining financial advantage by deception, engaging in conduct that corrupts a betting outcome and use of corrupt conduct information for betting purposes as well as animal cruelty.
“All codes of racing are very important to our state, very important to jobs, very important particularly in regional Victoria and all of that is based upon the integrity with which everyone in that industry plays their part,” Premier Daniel Andrews told reporters.
Several Weir-trained horses are due to race in Victoria later on Thursday and over the weekend.