Jean Richer and Leslie Sinobert argued the Correctional Service of Canada is violating their rights.
The two men told court they are in a "long-standing" relationship and want to live in the same house in the minimum-security annex at the federal Saskatchewan Penitentiary in Prince Albert.
Court heard they are serving life or indeterminate sentences, and were transferred from medium-security to the minimum Riverbend facility in the spring. They were then assigned to live in different housing units.
Prison officials denied a request by the couple that they be allowed to live under the same roof, stating the men get enough time during the day to see each other in common areas such as the gym or cultural centre.
They also said Sinobert needs to be in a separate home specifically for inmates with mental-health issues.
Prison policy states inmates cannot be in a house other than the one they've been assigned to.
Guards discovered Richer in Sinobert's house in July and he was convicted of a disciplinary offence. He was fined $5 for the unsanctioned visit.
Court heard Sinobert, 62, has had three strokes in the past decade and has suffered the effects of mercury-poisoning since he was a child. The court decision provided no details on Richer.
The couple did not have a lawyer. Richer represented both himself and his partner in court.
The couple's application went as far as to ask for unconditional release from the prison due to a "threat" to their liberties.
Justice Mona Dovell ruled she has no jurisdiction to determine if a prison's administrative decision is unreasonable. She also said the application process is "not a channel for drawing our court into the day-to-day management of a prison."
Had she decided she did have authority over the case, the judge said the couple would have lost anyway.
"The applicants have not established any deprivation of liberty, and the respondent has established that any possible deprivation of liberty is lawful," Dovell wrote in her decision.
"Not every constraint on an inmate amounts to a 'deprivation of liberty.'"
She recommended the couple file a grievance with the Corrections Department. If they are unhappy with the result, they could take their case to the Federal Court.
— By Chris Purdy in Edmonton
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