Apiarist Murray McGregor, the owner of Denrosa Apiaries in Blairgowrie, is the first person in the UK to be convicted of the charges.
The 61-year-old previously admitted administering "unauthorised veterinary medicinal products".
McGregor has produced honey for both the Balmoral Estate and Prince Charles' Duchy Estate.
Perth Sheriff Court was told that McGregor's colonies of bees had become infected with European Foulbrood
McGregor was told he would be given officially approved antibiotics to treat the disease.
But the court was told that he did not wait for the authorities and instead bought unlicensed Terramycin from the United States over the internet.
He admitted committing the breach between July 2009 and October 2010.
During the period, McGregor admitted importing the unauthorised medicinal product, Terramycin 100MR.
He also admitted giving Terramycin 100MR to an animal, namely the honey bee, in contravention of the relevant regulations.
He admitted a third charge of possessing the substance without authorisation.
The court was told that McGregor had kept bees since 1973 and took over the business in 1981.
Solicitor Kevin Lancaster, defending, said: "He admitted he was solely responsible for importing the Terramycin.
"He instructed administering the Terramycin to the bees.
"He accepts he did not get a veterinary prescription. He accepts he did not keep records."
Mr Lancaster said the company was the largest bee firm in Scotland.
He said: "It is a family company with 3,000 hives of bees in Scotland and parts of England.
"It was identified by Mr McGregor that some of the colonies were showing signs of disease. The scale of this was unprecedented within the industry.
"Further tests showed it was widespread. The disease continued to spread.
"If left unchecked it would effectively decimate the bee population. Burning all the hives was not a viable option."
The court was told that powder was placed in the hives and ingested by the bees, and that it posed no risk to the human food chain.
Sheriff Lindsay Foulis said: "The penalty imposed has to be at such a level to make it clear these regulations, or red tape, have to be complied with.
"They are in place for a reason."
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