Charges in a long-running case over the abduction of prized sheep from an Ontario farm were stayed this week, after a judge found there had been unreasonable delays in bringing the matter to trial.

The development ends a slow-grinding legal ordeal for an Ontario sheep breeder and a dairy farmer, unless the Crown decides to appeal.

Linda "Montana" Jones and Michael Schmidt were charged following an investigation into the removal of 31 sheep from an Ontario farm in April 2, 2012, hours before the animals were to be euthanized.

The Canadian Food Inspection Agency had ordered the slaughter after a sheep sold by Jones to an Alberta farm allegedly tested positive in 2010 for scrapie, a deadly and easily transmitted disease that affects the nervous systems of sheep and goats.

A lawyer for Jones and Schmidt sought a stay of proceedings earlier this month, arguing the delay in bringing the case to trial was unreasonable.

The application was made in line with a Supreme Court of Canada ruling earlier this year that concluded delays must not exceed 30 months in superior courts and 18 months for cases at the provincial level.

The judge presiding over the case agreed the delay was unreasonable and stayed the charges against Jones and Schmidt this week.

Justice Laura Bird said the delay was largely the result of difficulties in Crown disclosure to the defence, and noted that the CFIA, in her view, did not devote sufficient resources to the management of the file.

A trial for Jones and Schmidt was set to begin in April 2017.

"The total delay between the date the information was sworn and the expected completion of the trial is four years and five and a half months," Bird wrote in her ruling. "The applicants have established on a balance of probabilities that their right to be tried within a reasonable time ... has been infringed."

Jones faced six charges -- five under Health of Animals Act and one charge of conspiracy under the Criminal Code -- while Schmidt, who has previously clashed with authorities over the right to sell raw milk, faced two charges under the HAA and one conspiracy charge under the Criminal Code.

"To have this case go on...just for it to have turned into this for seven years, it's tragic," Jones said after Bird's ruling. "Even though we've won today I don't want to walk away from it as if it never happened."

When the CFIA learned of the positive test for scrapie on the Alberta farm, it made a number of orders which affected Jones' farm and her herd of Shropshire sheep, Bird's ruling said.

On March 23, 2012, an order was signed authorizing the destruction of 41 sheep, an action that was to take place on April 2 that year.

Ten of the sheep were found either dead or dying during an inspection a few days later and were removed from the property, Bird's ruling said.

Jones said, however, that there were no dead or dying sheep on the farm. She said a group of young sheep that were on the CFIA destruction order were sent to an abattoir on the advice of the CFIA, which authorized them to be processed and sold for meat. Jones said she chose not to sell any freezer lamb at the time.

On April 1, 2012, the remaining 31 sheep that were to be killed were suddenly taken from Jones' farm by a group that called itself the Farmers Peace Corp.

"This was allegedly done by Mr. Schmidt, who was acting with others, with the knowledge and consent of Ms. Jones, to prevent the sheep from being destroyed," Bird wrote.

"It was the removal of the sheep on April 1, 2012 that turned this matter into an investigation as opposed to the regulatory process that it had been until that point."

Jones' lawyer said her client had tried to negotiate with the CFIA to either keep her farm under quarantine permanently or, if her sheep had to be killed, to save some of the animals' genetic material.

"These are Shropshire sheep that have some relatively rare genetics," said Genevieve Eliany. "Because negotiations with the CFIA were impossible, the Farmers Peace Corp came along and removed the sheep the night before they were supposed to be taken and euthanized."

The sheep abducted from Jones' farm were eventually found, killed, and all tested negative for scrapie, Eliany said.

The Crown had argued that the one infected sheep on the Alberta farm -- known as 24S -- came from Jones' farm, Bird's ruling said.

Lawyers for Jones and Schmidt contested this and argued the Crown could not prove that 24S was positive for scrapie, saying there were alleged deficiencies in testing procedures and it was possible another sheep from the farm actually had the disease.

The defence also suggested the Crown could not prove that 24S had the disease when it was sold by Jones and even if it was in fact infected with scrapie, it may have been exposed to the disease after arriving in Alberta.