The force said several items were seized including a firearm and conductive energy device, which can be known in racing circles as a jigger.
Racing Victoria said it had been investigating "the activities of licensed persons" and brought in Victoria Police.
"During the course of our investigation, we sought the support of Victoria Police's sporting integrity intelligence unit on the matter, instigating their investigation," executive general manager of integrity Jamie Stier said in a statement.
"As the matters are the subject of ongoing investigations by Victoria Police and Racing Victoria we are not at liberty at this time to disclose the identities of the persons arrested nor the details of the investigations.
"Racing Victoria is committed to maintaining the highest integrity standards in our sport and, where appropriate, we will continue to work with Victoria Police on those investigations."
Weir is one of Australia's best-known horse trainers and was behind the 2015 Melbourne Cup winner Prince of Penzance.
He's Australia's most prolific and successful trainer.
Weir has re-written the record books for winners trained in a season and just this week was at the Karaka sales buying yearlings to be raced in Australia.
When driven away from the Ballarat police station yesterday afternoon, Weir was seen to be smiling and even gave television cameras covering his arrest the thumbs up.
Victorian Racing Minister Martin Pakula said the investigation showed authorities were enforcing rules "without fear or favour".
"As minister for racing and a racing lover, I'm committed to maintaining the integrity of our sport and any allegations of breaches are extremely disappointing," he said in a statement.
Weir's stable had six horses entered for the Mornington meeting in Victoria yesterday and all were allowed to start.
- NZ Racing Desk
