The judge in a case challenging Canada's solitary-confinement system has pointedly questioned whether the way it is supposed to run matches reality, particularly when it comes to inmates who want to challenge their placement in a segregation cell.

The BC Civil Liberties Association and the John Howard Society of Canada have sued Ottawa over the use of solitary confinement in federal prisons, arguing it is unconstitutional, increases inmates' suffering and discriminates against offenders who are Indigenous or have mental illness.

Counsel for the Attorney-General of Canada began its closing submission in the B.C. Supreme Court case Wednesday, arguing segregation is a reasonable and necessary tool that protects inmates and staff and is only to be used as a last resort.

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Read more: How four people's stories have changed hearts, minds and laws on the issue of solitary confinement

But Justice Peter Leask challenged the government on its view that any prisoners who want a lawyer at their segregation hearing can have one, saying that did not reflect the situation on the ground.

"These are muddy waters, counsel," Justice Leask said. "I know you're being sincere in your submissions but I'm not so sure you're describing the reality of the conditions very well."

The court has heard evidence on how difficult it can be for inmates to challenge their placement in solitary. Amanda Lepine told the court she was placed in segregation at Edmonton Institution for Women in January for allegedly assaulting another inmate. She denied she had done so but spent 26 days in solitary nonetheless and saw her classification raised from medium security to maximum security, a change that was not made clear to her until about three weeks later. Ms. Lepine said she filed a grievance in late January or early February but a ruling in her favour was not delivered until late May.

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Justice Leask told counsel for the federal government he was not aware of a segregation review hearing in which a lawyer had been present. In fact, he said, some of the evidence indicated Correctional Service Canada preferred it that way.

Mitchell Taylor, one of the lawyers for the federal government, said the law stipulates every inmate shall be given a reasonable opportunity to retain and instruct legal counsel without delay. He said all inmates are informed of their right to counsel when placed in segregation.

Mr. Taylor said an inmate who wanted a lawyer at a segregation review hearing could push for it.

"I'm not with you there," Justice Leask said. "There's no evidence that anybody at CSC treats it that way. There's some evidence that they treat it in the opposite way."

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The judge went on to say inmates have little money to spend on a lawyer.

"The right of a penniless prisoner to retain and instruct counsel without delay seems pretty empty to me," he said.

Justice Leask said he was "not completely happy" with the impact of "this reasonable sort of regulatory language" for actual prisoners. He questioned what "teeth" the grievance process has.

The judge later said Correctional Service Canada could do better when it comes to treating those with mental illness. He said he was concerned by the lack of data on the subject.

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Counsel for the plaintiffs in the case finished its closing argument Tuesday. It said solitary confinement causes psychological harm to nearly everyone who endures it and has been a factor in several prison suicides. It said if segregation has to exist in Canada, it must come with stricter limits, including a hard cap on 15 consecutive days in solitary. That would be in line with the United Nations' Mandela Rules, which define prolonged solitary confinement as a period lasting more than 15 days.

The Globe and Mail has reported extensively on the prevalence and effects of solitary confinement, beginning with a 2014 investigation into the suicide of Edward Snowshoe after 162 consecutive days in segregation.

But Mr. Taylor said a hard cap would apply an arbitrary limit to a placement that could be immensely complicated. He said such a cap could also raise its own Charter issues for those who want to be kept in segregation for their own safety.

Justice Leask said CSC has come to ignore the distinction between who wants to be in solitary and who doesn't. He said that doesn't have to be the case. "It may be that following the law, voluntary people don't [factor into] this regime at all, right?" he asked.

The trial has focused on the current solitary-confinement system, not a new bill introduced by the federal government in June. The bill says an inmate can spend no more than 21 consecutive days in segregation, though a warden could order otherwise. Eighteen months after passage, the cap would drop to 15 days. The BCCLA has said both the current system and the new bill fail to guarantee an individual will not be held in solitary for years.

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Mr. Taylor said the solitary-confinement system is sound. He said it is aimed at maintaining security, as well as the rehabilitation and reintegration of inmates. "It's a regime that has a lot of robustness and rules about it. It's not a situation where they're put in and there are no parameters that govern what has to be done," he said.

Counsel for the federal government is expected to continue its argument Thursday.