One of Canada's top courts ruled Wednesday that an agreement with Washington barring people from seeking asylum if they arrive from US soil is invalid because it violates migrants' rights.

The controversial 2004 deal, known as the Safe Third Country Agreement (STCA), says anyone applying for asylum in either the United States or Canada must file their application in whichever country they enter first.

However, a federal court judge ruled the pact violates the Canadian Charter of Rights and Freedoms.

"Everyone has the right to life, liberty and security of the person and the right not be deprived thereof," Judge Ann Marie McDonald wrote, citing the Charter.

The agreement has been repeatedly denounced by rights' groups, and asylum seekers challenged it by arguing that the United States under President Donald Trump could no longer be considered a "safe" country.

To skirt the rule and guarantee their asylum application will be considered in Canada, tens of thousands of migrants have passed into the country through unofficial border crossings such as at Roxham Road, an area on the border between New York and Quebec.

The ruling does not take effect for six months, during which time the government will be given a chance to reply. The ruling can also be appealed to a federal appellate court or the Supreme Court.

- 'Cannot be justified' -

McDonald's ruling cites the case of a female Muslim immigrant from Ethiopia named Nedira Mustefa, who was held in isolation for one week at a US detention center after being returned by Canadian authorities. Mustefa described the experience as terrifying and traumatizing.

"Ms Mustefa was returned to the US where she was immediately imprisoned," the judge wrote.

"In my view, the risk of detention for the sake of 'administrative' compliance with the provisions of the STCA cannot be justified.

"Canada cannot turn a blind eye to the consequences that befell Ms Mustefa... The evidence clearly demonstrates that those returned to the US by Canadian officials are detained as a penalty."

Since Donald Trump became US president in January 2017, tens of thousands of people have crossed from the United States into Canada seeking asylum.

The rights group Amnesty International praised the court's decision.

The STCA "has been the source of grave human rights violations for many years, unequivocally confirmed in this ruling," said Alex Neve with Amnesty International Canada.

"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," Neve said in a statement.

Neve called on Canada to revoke current restrictions "which practically closes the border to refugee claimants as part of Canada’s COVID-response."

A spokesperson for Minister of Public Safety Bill Blair said the government is evaluating the ruling, noting that it will not go into effect until January 2021.

In the meantime, the STCA remains in effect, the spokesperson said.