A Federal Court justice says the Safe Third Country Agreement — Canada's asylum agreement with the United States — infringes upon the Canadian Charter of Rights and Freedoms and is giving the federal government six months to respond.

Justice Ann Marie McDonald said the agreement — which stops people from entering either Canada or the U.S. at official Canada-U.S. border crossings and asking for asylum — violates the section of the Charter guaranteeing "the right to life, liberty and security of the person"

The case was brought forward by the Canadian Council for Refugees, Amnesty International, the Canadian Council of Churches and a number of individual litigants who argued that by returning ineligible refugee claimants to the U.S., Canada exposes them to risks — including detention and eventual deportation to countries where they could face harm.

"The applicants have provided significant evidence of the risks and challenges faced by STCA ineligible claimants when they are returned to the U.S.," McDonald wrote.

"The evidence establishes that the conduct of Canadian officials in applying the provisions of the STCA will provoke certain, and known, reactions by U.S. officials. In my view, the risk of detention for the sake of 'administrative' compliance with the provisions of the STCA cannot be justified."

The 16-year-old agreement recognizes both countries as "safe" countries for migrants and states that refugee claimants are required to request refugee protection in the first country they arrive in — meaning Canadian border officials would send back to the U.S. any would-be refugee claimants arriving at an official border crossing into Canada.

One of the applicants in the case, Nedira Mustefa, is a Muslim woman from Ethiopia who was detained in the U.S. after her attempt to enter Canada. She was held in solitary confinement for one week.

According to the court decision, Mustefa described her time in solitary as "a terrifying, isolating and psychologically traumatic experience."

"Ms. Mustefa, who is Muslim, believes that she was fed pork, despite telling the guards she could not consume it for religious reasons," reads the document. "Mustefa describes skipping meals because she was unable to access appropriate food, and losing nearly 15 pounds."

Mustefa told the court she "felt scared, alone and confused at all times" and that she "did not know when [she] would be released, if at all."

In her decision, McDonald said she found the evidence clearly demonstrates that those returned to the U.S. by Canadian officials are "detained as a penalty."

"Canada cannot turn a blind eye to the consequences that befell Ms. Mustefa in its efforts to adhere to the STCA," she wrote.

The government — the respondents in the case — argued that while failed claimants are subject to detention in the U.S., there is a fair detention review process available. McDonald rejected that argument.

"Suggesting that those who are imprisoned will eventually be released is not sufficient evidence of minimal impairment," she wrote.

The government also argued that striking down the agreement would lead to an increase in claims and put the overall refugee system at risk.

"However, in my view, the evidence offered by the respondents on this point is weak," wrote the justice. "In the past, Canada has demonstrated flexibility to adjust to fluctuations in refugee numbers in response to needs."

The agreement has come under intense scrutiny since U.S. President Donald Trump's administration began tightening asylum rules.

Advocates have argued the Trump administration's actions mean the U.S. is no longer a safe harbour for those seeking asylum.

McDonald ruled the agreement invalid but has suspended that declaration for six months to allow Parliament to respond.

A spokesperson for Public Safety Minister Bill Blair said the department is "aware of the Federal Court's decision and [is] currently reviewing it.

"Although the Federal Court has made its ruling, that decision does not come in effect until January 22, 2021. The Safe Third Country Agreement remains in effect," said press secretary Mary-Liz Power.

The three groups which brought the case are asking the government to stop returning refugee claimants to the U.S. in the meantime.

"While the Federal Court has provided the government with six months leeway, it is imperative that Canada immediately end the return of claimants to the U.S.," said Alex Neve, secretary general for Amnesty International Canada, in a joint statement.

"The Safe Third Country Agreement has been the source of grave human rights violations for many years, unequivocally confirmed in this ruling. That cannot be allowed to continue one more day, and is of even greater concern now given the prevalence of COVID-19 in immigration detention in the United States."

Conservative MP Peter Kent, the party's critic for citizenship and immigration, is calling on the government to appeal the decision. The NDP's immigration critic, Jenny Kwan, wants the Liberals to do no such thing.

"We hope the Liberals will accept this important decision and not appeal it since too many people have already lost their rights," she wrote in a media statement.

"The Liberal government must now give notice to the U.S. immediately and withdraw from the Safe Third Country Agreement to stop being complicit in forcing asylum seekers to return to persecution, torture and even death."