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A group of asylum seekers cross the Canadian border at Champlain, N.Y., Aug. 4, 2017.Ryan Remiorz/The Canadian Press

Canada’s ambassador to the United States says “legitimate refugee claimants” should make their claims through an “appropriate” process rather than crossing from the U.S. between official points of entry.

David MacNaughton said the U.S. moving to begin the process to renegotiate the Safe Third Country Agreement is an encouraging sign. Ottawa wants the pact changed to close a loophole in order to allow Canada to quickly turn away most asylum seekers coming from the United States who enter from unauthorized points.

Asked to square this request with the federal government’s position that refugees are welcome in Canada, Mr. MacNaughton said asylum seekers should use an “established” process.

“We’re open to immigration. We’re also open to legitimate refugee claimants who go through the process that is established,” Mr. MacNaughton said Tuesday in the U.S. Capitol after a lunch meeting with legislators on trade. “What we’re trying to do is make sure that those who are wanting to claim refugee status do so in the way in which it’s appropriate.”

More than 40,000 asylum seekers have entered Canada through unofficial points of entry since U.S. President Donald Trump launched his crackdown on illegal immigration two years ago. The flood of claimants is bogging down the refugee protection system in Canada.

Under the current pact, most refugee claimants who come to Canada from the United States through official points of entry – such as border stations – are immediately sent back to the United States, as it is considered a safe country for refugees under the treaty. But the agreement does not apply between such points of entry, so those who cross between border stations have the right to make a refugee claim.

Mr. MacNaughton said he is encouraged that the United States is starting to move on renegotiation. But he said he did not know whether the United States would agree to the rewrite Canada wants.

“We have had no firm indication as to what they’re prepared to do or not do,” he said. “It’s a positive thing that it’s gone to State [Department] to give a negotiating mandate because that hasn’t been the case for the last however long we’ve been asking for this to happen.”

Canada has been pressing the United States to renegotiate for more than a year. The U.S. Department of Homeland Security is now working with State Department officials on a formal request to reopen the deal, The Globe and Mail reported on Monday. An assistant secretary would have to authorize the request for talks to start.

Border Security Minister Bill Blair has proposed a change to the agreement that would see Canadian border officials take such asylum seekers to an official crossing, where they would be denied immediate entry. But that plan would have to clear legal hurdles articulated by the Supreme Court that guarantee a hearing to any refugee claimant setting foot in Canada.

Janet Dench, executive director of the Canadian Council for Refugees, said a renegotiation could backfire on Canada. She said Canada risks drawing Mr. Trump’s attention to the 2004 border agreement, which could lead the United States to propose changes to the agreement that Ottawa doesn’t want.

“This agreement was negotiated to favour Canadian interests and at Canadian request,” Ms. Dench said. “And so in asking to renegotiate the agreement, the Canadian government must be aware that the U.S. government may ... actually want to negotiate it so that fewer refugees are sent back to the U.S. or that the U.S. would think maybe we should actually withdraw ourselves from this agreement.”

The CCR, along with Amnesty International and the Canadian Council of Churches, launched a Federal Court challenge to the agreement in 2017, arguing against Canada’s position that the United States is a safe country for refugees under the Trump administration. A decision has not yet been issued by the court.

The NDP has called on the Liberals to suspend the pact so asylum seekers in the United States can claim refugee status at official Canadian land border posts.

Conservative immigration critic Michelle Rempel urged the Liberal government to act immediately to stop the flow of asylum seekers between official points of entry along the border, saying she doesn’t buy its assertion that Canada can’t make the appropriate changes without agreement from the United States. She accused the Liberals of putting forward ideas without a plan to practically implement them.

“We’re six months out to an election and after trying to make electoral hay out of calling Canadians who raise questions about this fear mongerers and un-Canadian and thinly veiled accusations of racism, I think that this is now about electoral calculus rather than action,” Ms. Rempel said.