Trainers Danny O'Brien and Mark Kavanagh are victims in their long-running cobalt saga and should not be punished should Racing Victoria win an appeal on points of law, a court has heard.

Three Court of Appeal judges are deciding whether to resurrect any cobalt offences against the two Flemington trainers after the charges were dismissed by the Victorian Civil and Administrative Tribunal.

Should Racing Victoria succeed in its appeal on two points of law around the interpretation of the rules of racing, the case would be sent back to VCAT to determine any penalty.

VCAT president Justice Greg Garde concluded that while there was no doubt cobalt was administered to four O'Brien-trained horses and one from the Kavanagh stable in in late 2014, the trainers had no knowledge of it.

It was clear they were victims of veterinarian Dr Tom Brennan and had no knowledge, inkling or suspicion that the vet intended to use a substance called vitamin complex in drips for their horses, the judge said in March.

Court of Appeal Justice Anthony Cavanough said given Justice Garde found the trainers had no inkling or suspicion, "presumably any penalty would have to be fashioned accordingly" should the matter go back to the VCAT president.

O'Brien and Kavanagh's barrister Damian Sheales said Justice Garde had found the trainers were victims.

"It's difficult to see how they should be reprimanded in these circumstances," he said on Friday.

Justice Garde overturned O'Brien and Kavanagh's respective four- and three-year disqualifications for administering cobalt.

He ruled the test results that showed cobalt above the permitted threshold were inadmissible because Racing Victoria's procedure for testing for cobalt from April 2014 to August 2015 substantially departed from the racing rules.

The judge said he would have found O'Brien and Kavanagh guilty of the lesser charge of presentation if the test results were admissible.

Racing Victoria is challenging the ruling on admissibility and wants the Court of Appeal to determine the appropriate level of responsibility a trainer must have for the management of their horses and service providers.

Racing Victoria argued there was ample evidence to prove the horses had elevated cobalt levels beyond the testing certificates.

Its barrister Paul Holdenson QC said the horses' elevated cobalt readings were found to be accurate.

The Court of Appeal reserved its decision.