More than three years after it began, the cobalt case against trainers Mark Kavanagh and Danny O'Brien has ended with the two fined $4000 and $8000 respectively.

Justice Garde of the Victorian Civil and Administrative Tribunal delivered his decision on penalty on Tuesday after the two were originally disqualified by racing authorities for the administration of cobalt to horses in their care.

VCAT overturned the bans and Racing Victoria took the case to the Court Of Appeal which agreed they should be penalised for presentation but that neither had knowledge of administration.

Dr Tom Brennan, the vet who attended both Flemington stables, was found to have administered a drip containing illegal levels of cobalt without the trainers' knowledge.

Brennan has denied knowing the supplements he was giving the horses contained cobalt.

In his judgment, Justice Garde said the financial losses incurred by the trainers since the case began were substantial.

"Kavanagh's business lost $200,000 over a two year period," the judgment said.

"Whereas prior to 14 January 2015 he had 35-40 staff, by the time he gave evidence to the Tribunal in October 2016 he had only 10 staff. His stable of about 120 horses had reduced to 25 horses."

He said O'Brien's stable of 180-200 horses had reduced to 70-75 over the same period and his staff from 50 to about 30.

Under the Rules of Racing regarding prohibited substances detected on race day, the horses involved have been disqualified from their respective races and the prize money forfeited.