The prosecution said it was not in the public interest to bring a second case against breeder Bobby Waugh, for allegedly breaching animal movement restrictions.
Mr Waugh, 57, from Sunderland, was convicted in May of breaching a series of animal health regulations at his farm at Heddon-on-the-Wall, Northumberland.
He was banned from keeping any livestock for 15 years.
'Poor health'
At a pre-trial review on Monday at Hexham Magistrates Court, Northumberland County Council formally told Mr Waugh it would not bring a new case against him.
It had been considering allegations relating to breaches of animal movement regulations before the outbreak in February 2001, which Mr Waugh has denied.
Tom Finch, prosecuting, told the hearing the farmer had already been punished by the courts, was in poor health and had financial difficulties.
But charges relating to alleged illegal movement of animals against haulier Leslie Scurr, 37, of Ripon, North Yorkshire, have not been dropped.
He faces 11 charges under the Animal Health Act and the Trade Descriptions Act alleged to have been committed on February 15, 2001.
'Career over'
Speaking outside court, Mick King, of Northumberland County Council Trading Standards department, said it did not believe it was in the public interest to continue the case against Mr Waugh.
"At an earlier trial in May of this year Bobby Waugh was convicted of some of the most serious animal health charges that exist," Mr King said.
"He has already received a 15-year ban from keeping livestock, which effectively ends his career in farming."
After the hearing Mr Waugh said he was delighted the charges had been dropped.
Depressed animals
He also maintained his innocence against the allegations.
During the first trial a video was shown of the Mr Waugh's pig fattening unit, where foot-and-mouth disease was found after it was traced from an Essex abattoir.
Animal experts at the trial said he should have spotted that his depressed animals were sick and notified the authorities.
The case against Mr Scurr was adjourned until February 17 at Hexham Magistrates Court.