Kristi Miller told a federal inquiry Thursday that she learned about the gag order only through the inquiry and believes officials with the Department of Fisheries and Oceans were OK with her giving interviews about the publication of her article in the journal Science.
"I learned only through the inquiry process that the decision of not allowing me to speak to the press after the Science paper came out came out of the Privy Council Office and not from DFO," she said.
"I had permission to speak from the deputy minister and, I believe, the minister's office, so what I was not aware as a scientist is at what level these decisions are made."
Miller testified she believes it would have been useful to speak to the media after the article's publication to let them know what scientists knew and didn't know and she found it frustrating to see the direction some news stories went.
The federal government did not dispute Miller's suggestion that it was the Privy Council Office, which serves the prime minister, that refused to allow Miller to talk to media.
"Dr. Miller's testimony was thorough, extensive and speaks for itself," Dimitri Soudas, communications director at the Prime Minister's Office, said in an email to The Canadian Press.
"Her study and transcripts of her testimony is publicly available. . . The government will not interfere with Justice Cohen's work."
Miller testified senior officials had not prevented her from publishing work but stopped her from talking to the public because of the inquiry.
The inquiry heard Wednesday that Miller is working on trying to figure out whether the parvovirus is linked to the Fraser River sockeye collapse.
The virus has never before been found in fish and her work is considered groundbreaking.
Tim Leadem, legal counsel for the Conservation Coalition, a group of seven different organizations, said Thursday he doesn't know why officials close to the prime minister would become involved.
"Do we know the reason why the PCO needs to get involved at this level of spinning what stories should be emanating from a scientific journal publication?" he asked.
"I think those questions should be put to the prime minister to find out why his hands and his reach of his office has to go down to this level."
Miller suggested one reason scientists were advised not to attend sockeye salmon meetings that could be attended by members of the media.
She said researchers knew a disease may be present but they didn't know whether it was affecting farmed fish or other salmon species.
"I think the worry by the department was that if we bring out that there could be a disease issue in sockeye salmon without really understanding how far and widespread it might be. . . the worry would be that it would automatically be assumed to be associated with aquaculture, and we really didn't even have any data at that time," she said.
Miller also clarified comments she made Wednesday.
Under cross-examination by Gregory McDade, lawyer for the Aquaculture Coalition which opposes fish farms, Miller said the parvovirus could be the "smoking gun'" when it comes to the decline of Fraser River sockeye in 2009.
"Actually, I had no intention of saying that in this hearing," she said. "I felt a little bit backed into the corner on that one."
She said the virus could be a major factor, but not the only one involved in the decline of sockeye salmon.
Miller also told the inquiry that funding is an issue at her lab. She said her lab gets outside money from, among others, the Pacific Salmon Commission, which helps keep 11 people employed.
But a recent interpretation about whether external sources can pay the government scientists to test fish has thrown the lab's finances into question.
"It is a department-wide issue but there is no other single lab that has more than one or two staff members that have this issue," she said.
Miller said the issue has been ongoing for about 18 months.
In later testimony, four fisheries experts told the inquiry that for the most part, there's no link between salmon farms and sockeye spawning returns.
Their individual reports relied on data, including some from the B.C. Salmon Farmers' Association and the provincial government, to conclude that between 2003 and 2010, salmon farms reported a significant decline in the number of high-risk diseases.
Josh Korman, a fisheries ecologist with the firm Ecometric Research, said the majority of salmon that returned to the Fraser River in 2009 swam past the fish farms as smolts in 2007.
He said he's found the quality and amount of information available to be "impressive."
"What you have is an industry-reporting system that's fairly detailed, that's on a monthly basis across all farms and then an auditing system by provincial regulators that basically provides an independent estimate of disease and lice and other fish-harm health factors," he said.
Brock Martland, a lawyer for the commission, asked two experts whether they would declare a finding of innocence if the findings involved the criminal trial of a person.
Lawrence Dill, whose research focuses on behavioural ecology and parasites and fish farms, said sockeye can be exposed to pathogens transferred through waste from salmon farm processing plants or the environment.
"So I would not, at this point, be able to come down on the side of innocence," he said.