The Prince Edward Island facility is designated by the World Organization for Animal Health, known as the OIE, as one of only two international reference laboratories focusing on infectious salmon anaemia.
The lab and the efforts of researcher Fred Kibenge received national attention after his work on samples from B.C. sockeye salmon, work that was later challenged by the federal government.
Kibenge's research showed the presence of the virus that can be devastating to farm fish and has never been detected in British Columbian waters before.
Guy Gravelle, a spokesman for the Canadian Food Inspection Agency, said in an email Friday that an OIE member country had become concerned because the facility's work on samples from that country were not consistent with findings from other researchers.
He wouldn't name the country.
Don Reynolds, dean of the veterinary college, said the OIE then audited the lab this past August.
"We have that report," he said. "And there is a recommendation that says that until certain things are straightened out, so to speak, the OIE designation will be suspended and put into abeyance."
Reynolds didn't elaborate on what needs to be "straightened out," but added the recommendation must go to the OIE director who'll make a decision on the lab's designation.
"We're waiting here. We don't know when that will happen."
Reynolds said the college doesn't believe the recommendation has anything to do with Kibenge's testimony at the Cohen Commission, the federal inquiry examining the decline of Fraser River sockeye returns, or his work on the virus in British Columbia.
"We don't feel that way," he said. "We feel it's the result of the OIE audit."
At least one environmental organization, the Friends of the Earth Canada, is calling for an independent investigation of the food-inspection agency, saying the agency is trying to "silence" Kibenge, even though, as Reynolds said, the OIE, not the agency, made the recommendation to suspend the designation.
"This can only be a witch hunt against someone who doesn't agree with the government line and is suffering from the government's bullying," Beatrice Olivastri, a spokeswoman for the group, said in a statement to media.
The group argues decertification would reduce the ability of Canadians to know about the disease in salmon and could have an international impact because people in other countries send samples to Kibenge's lab.
The complaint that sparked the OIE audit was not the first time scientists have called Kibenge's work into question.
After Kibenge's lab found ISA in two of 48 sockeye salmon smolts last year, the Department of Fisheries and Oceans conducted its own tests, which concluded ISA was not present in British Columbia. Those results were verified by an independent lab in Norway.
In November 2011, Paul Kitching, B.C.'s chief veterinary officer, told reporters that anyone who said the virus was present in the province, based on results from the PEI lab, was misrepresenting the science.
The sample size, he added, was just too small.
"I can also say that as editor-in-chief of an international veterinary journal, this would be considered poor science and not likely publishable," Kitching said at the time.
Kibenge told the Cohen Commission in December 2011 that after he released his findings on ISA in B.C., the CFIA audited his lab, a procedure that took place months before the OIE audit.
He told the inquiry that officials were attacking his reputation and trying to discredit his work during the CFIA audit.
"Based on the questioning I got, I sensed that the interest here was to confirm my result was the result of contamination," he said.
"The second point was that probably I was doing shoddy science."
The OIE is an intergovernmental organization dedicated to improving animal health worldwide. It traces its roots back to 1924 and includes 178 member countries.