Justice Anne Mactavish raised the issue on the last day of a legal challenge launched by Canadian Doctors for Refugee Care and the Canadian Association of Refugee Lawyers.
The groups argue the changes announced 18 months ago are unlawful and inhumane, and want the court to strike them down.
Government lawyers say the new rules bring health benefits for newcomers in line with what other Canadians receive, and deter those who would abuse Canada's health-care system.
They have argued refugee claimants can still access health care through other programs, including those put in place by some provinces to reinstate access to essential and emergency care.
But though Alberta, Manitoba, Saskatchewan, Nova Scotia, Quebec and Ontario have all taken steps to bridge the gap, not all offer the same level of coverage.
While Ontario has put forth a "coherent program," Mactavish said, Quebec offers assistance on an ad-hoc basis, which can leave refugee claimants dependent on the "whims" and "charity" of officials.
"Is that filling the gap?" the judge asked. And "is it humane to put people through that?"
Neeta Logsetty, one of the government lawyers, said many refugee claimants had also received donations from pharmaceutical companies and help from doctors, as well as provincial assistance.
Of those involved in the court case, "everyone got the treatment they required, at little or no cost," she told the judge.
What's more, she argued, many Canadians also face hurdles in accessing health care.
"The reality is the health-care system isn't perfect in Canada," she said.
"Many Canadians and permanent residents, they face many similar issues" as refugee claimants, she said.
Lawyers for the doctors and lawyers maintained the cuts put refugee claimants through severe psychological distress, and there's no way to ensure they'll always receive the care they need.
"They (the government) cannot guarantee in any fashion that these services will be available in the future," Jacqueline Swaisland told the court.
Ottawa trimmed medical benefits for newcomers in 2012, leaving most immigrants with basic, essential health care but without supplementals such as vision and dental care.
However, rejected refugee claimants — and refugee claimants from countries the government considers safe — will be eligible for care only when they pose a threat to public health.
Ontario reinstated the benefits Jan. 1, a move that drew strong criticism from Ottawa, which accused the province of intruding into an area of federal responsibility.
Federal Citizenship and Immigration Minister Chris Alexander also called Ontario's move a "reckless" policy that threatened the success of reforms to the refugee system.
Government lawyers told the court that striking down the changes would "result in a policy vacuum" that could endanger refugee claimants as well as public safety.
Mactavish was expected to begin her deliberations Thursday but did not say when she would render her decision.
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