The County Laois-based trainer was fined €27,500 and ordered to pay €7,500 in legal costs after being found guilty of serious misconduct by the Irish Horseracing Regulatory Board arising out of a stable inspection which followed a positive cobalt sample from a winner he trained at Dundalk in January last year.
In conjunction with Department of Agriculture officials, an unannounced inspection of Cotter's yard was carried out on February 3 last year and, while hair and blood samples taken from all the horses in his care revealed no results of concern, he was found guilty of serious misconduct.
Cotter was fined €20,000 for failing to maintain his medicines register and a further €7,500 in rule breaches attached to the positive cobalt sample of Slade Runner, who had won at Dundalk but was subsequently disqualified. Legal costs brought his total bill to a whopping €35,000.
Cotter, whose speedy Matilda Picotte could run in the Queen Mary at Royal Ascot next month, does not believe the punishment fits the crime and is lodging an appeal to the IHRB against the severity of the fines.
Cotter told the Racing Post: "I realised certain standards fell short of what is expected and have made the necessary changes. As a licensed trainer for over 26 years with an unblemished record I fully engaged and cooperated with the enquiry from the outset.
"I'm therefore astounded with the severity of the disproportionate fines imposed and will appeal these."
Explaining how Slade Runner tested positive for cobalt, Cotter said: "My horse Slade Runner tested positive for cobalt on January 21 of last year and this happened because I treated him for a faecal issue with an over the counter product.
"I was horrified that it caused a five-billionth of a gram positive. That is the equivalent of a clock being five seconds wrong in 32 years. For this I received a €2,500 fine for administering it without veterinary advice. The standard fine for medicine register related offences is approximately €200-€800, yet my fine was €20,000!"
Four years ago Cotter teamed up with Danny Murphy, an experienced trainer on the international stage, and he explained to the committee the pair had formed a 50-50 business partnership. He described this as a positive move as before he was training what he called a bunch of "third division" horses.
Cotter has trained four winners from 41 runners this season. The aforementioned Matilda Picotte was an impressive winner of a Curragh maiden on debut before fading into fourth after showing blistering early speed in the Group 3 Fillies Sprint Stakes at Naas on Sunday. She is generally a 10-1 shot for the Queen Mary.