Victorian horse trainer Danny O'Brien wants the racing industry investigated after his cobalt ban was overturned, with a surprised Racing Victoria preparing its next legal move.

O'Brien and Mark Kavanagh had received respective four- and three-year disqualifications after five horses returned positive results for cobalt in 2014.

But Justice Greg Garde dismissed the cobalt charges against the trainers at the Victorian Civil and Administrative Tribunal on Friday.

The judge said there was a problem with the evidence that Racing Victoria had relied upon.

"The tribunal finds that over the period of April 2014 until August 2015, the procedure for testing for cobalt substantially departed from the requirements," Justice Garde said.

"The test results are inadmissible as evidence against the trainers."

Racing Victoria's acting chief executive Giles Thompson was disappointed with the judgment but maintains it was the right decision to continue with the case.

"We will take the time to consider the decision in full and therefore we won't comment on what the next steps are," Thompson told reporters on Friday.

"We lost the case on a technicality around the interpretation of a specific rule of racing.

"But it does not alter the fact that the horses at the centre of this had cobalt readings that could undermine the integrity of our sport."

During the trainers' appeal, which began in October 2016, their lawyers said the Perth-based ChemCentre and Hong Kong Jockey Club laboratories were not accredited to test for cobalt at the time five horses from their stables returned positive results.

Despite being disqualified, they continued to train horses under a stay of proceedings.

Outside VCAT, O'Brien said he knew he had done nothing wrong since the first positive cobalt result came back in 2014.

"When they came back, both Mark and I were adamant that we'd done nothing wrong," he told reporters.

He said Justice Garde's judgment confirmed their innocence.

"He's been very clear that neither Mark nor I had any intention of cheating or trying to break any rules of racing, that we're completely innocent of all charges," O'Brien said.

The trainer has criticised Racing Victoria's handling of their case, and says the state government needs to step in.

"The bullying and vilification of both Mark and I, and our families, by (chief racing steward) Terry Bailey and his integrity department has been quite incredible," O'Brien said.

"It's time that (Racing Minister) Martin Pakula took a hard look at what is going on in the racing industry in this state."

Justice Garde has directed the Racing Victoria orders against the trainers be set aside.

Thompson said Racing Victoria had sufficient evidence to prosecute and said Justice Garde agreed with that despite the dismissal.