Victorian trainers Lee and Shannon Hope have lost their long-running cobalt case, with an appeal judge finding both guilty over the deliberate and secret race-day administration of the substance.

Shannon Hope was well aware he was giving horses substances he should not be administering and his father knew and did nothing to stop it, Justice Greg Garde concluded.

The father-and-son training partners denied cheating but Garde found both guilty of administering prohibited substances to three horses to affect their performance in 2014 races.

In a decision released on Friday, Garde concluded cobalt-containing substances were administered to Windy Citi Bear, Best Suggestion and Choose on or shortly before race day.

Both trainers were well aware of the unrecorded administration of additional cobalt supplements or medications beyond what was disclosed and intended the use to occur, he said.

"I am satisfied that Shannon Hope, who had charge of the horses stabled at Seymour, was well aware that he was administering or causing the administration of substances that he should not be administering," Garde said.

Lee Hope was well aware of what his son was doing or arranging for the administration of supplements and medications on race day or close to race day, the judge said.

"Given the strength and closeness of the father-son bond over a long time, I do not accept that Shannon Hope concealed what he was doing in relation to the administration of supplements and medications from his father," Garde said.

"Lee Hope did not suggest that he did.

"I am satisfied on the balance of probabilities to a comfortable level of satisfaction that Lee Hope was aware what was happening within the stable, and took no step to stop or prevent unrecorded administrations of cobalt-containing supplements or medications."

The Hopes had blamed their feed and supplements regime for an inadvertent breach of the cobalt threshold, pleading guilty to a lesser administration charge during the appeal.

But Garde said race-day administration of cobalt-containing supplements or substances, whether intravenous or through feed or both, was the most probable explanation for the high test results.

He concluded it was to benefit the horses' race performance, saying there was no other conceivable reason why the trainers would administer substances on race day itself or the day before.

Garde said the administration of cobalt-containing substances was surreptitious, and was kept secret because the race-day administration of medications carried a minimum six-month licence disqualification.

After Shannon Hope admitted lying to the Racing Appeals and Disciplinary Board, Garde said the trainer's dissimulation on the important subject of his knowledge of the cobalt rules "leaves his credit open to grave doubt".

The RAD Board in 2015 disqualified Shannon Hope for five years and Lee for three years.

They will now face a penalty hearing in the Victorian Civil and Administrative Tribunal on a date to be fixed.

Racing Victoria and the Hopes declined to comment on Friday.