Dr. Shiv Chopra has lost his 13-year battle to regain the Health Canada job from which he was fired in 2004.
The ruling came from the Federal Court of Appeal on Wednesday.
Chopra called it a "travesty of justice."
Chopra was one of three Health Canada veterinary scientists who spoke out in the 1990s about pressure from their bosses to approve drugs despite concerns about human safety. He and his colleagues, Dr. Margaret Haydon and Dr. Gérard Lambert, were eventually fired in 2004 for insubordination.
One of the drugs Dr. Chopra spoke out against was bovine growth hormone, which is used to boost milk production. It remains illegal in Canada because of concerns about animal health.
'Last chance at justice'
Advocates for Chopra had called today's hearing his "last chance at justice."
In August 2011, the Public Service Labour Relations Board ruled Lambert had been dismissed unfairly and should be reinstated, but not the other two scientists.
The scientists' union, the Professional Institute of the Public Service of Canada, was supporting all three in their bids to get their jobs back, and its president at the time said he was "perplexed" about why only one would be reinstated, given that all three had been fired the same day and for the same reasons.
A later appeal to the Federal Court of Canada led to Haydon winning the right to return to work as well, though legal proceedings in her case are ongoing. That left only Chopra's firing for consideration by the Federal Court of Appeal.
Hearing turned on issue of progressive discipline
Chopra's hearing today was on the narrow issue of progressive discipline, a process by which punishments get more severe for employees with each infraction.
Prior to his firing, Chopra had received a 20-day suspension. He grieved that punishment and won. Chopra's lawyer David Yazbeck argued — without success — that the use of that wrongful suspension to justify the firing was not properly considered by the previous adjudicator.
Chopra's two former colleagues won the right to be reinstated because previous suspensions had been wiped from their records, Yazbeck said.
'Government has spent millions of dollars fighting me'
Chopra said the real loser in his case is the public.
"I've lost a lot of money, but so what?" he said. "The government has spent millions of dollars fighting me all these years. It's public money they are spending."
In his many years fighting Health Canada, Chopra also said the courts have never considered the actual content of his concerns about Health Canada, which include how it deals with hormones, antibiotics and slaughterhouse waste.
"At this point, the public will continue paying a very heavy price, with their health," he said.
Chopra praised his family for standing by him in his long fight, giving them credit for his very survival.
"A lot of people have heart attacks and die," he said. "That's what the department had been hoping from me, that I would die and disappear."
Lawyer David Yazbeck said the cases of Chopra and his two colleagues demonstrate the personal price that whistleblowers pay.
"If you want to blow the whistle you have to be prepared to risk your career," he said. "That includes financial damages, personal damages. Your family suffers as well."
Government considering changes to whistleblower laws
Yazbeck has testified at a House of Commons committee considering new ways to protect whistleblowers. The committee released its recommendations in June, and the government is expected to respond this fall.
But at age 83, with no ruling to allow him to return to work, Chopra is unlikely to benefit from new changes to whistleblower protection.
His last hope to regain his job rests with the Supreme Court of Canada, if he decides to seek leave to appeal. Yazbeck said such leave is rarely granted.