Boats have reportedly been stopped near islands of Machias Seal and North Rock as US agents search for undocumented migrants

Canada’s government is investigating reports that US border patrol officers have intercepted and questioned crew members on more than 20 Canadian vessels in disputed waters off the coast of Maine.

The reports have thrust a longstanding territorial dispute between the two countries into the spotlight; since the late 1700s tensions have simmered over a pair of tiny, treeless islands that sit between Maine and the Canadian province of New Brunswick.

Primarily inhabited by nesting puffins, the islands of North Rock and Machias Seal remain the only disputed lands between US and Canada, with both claiming sovereign jurisdiction over the islands and their surrounding waters. As a result, the area has long hosted lobster fisherman from both sides of the border.

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The question of jurisdiction flared up recently after the Grand Manan Fishermen’s Association said a Canadian vessel had been stopped by US border patrol while fishing in the waters near Machias Seal Island in late June.

“He informed them he was a Canadian vessel legally fishing in Canadian waters,” wrote Laurence Cook of the association on Facebook. He said he was “not surprised to see the Americans trying to push people around”, describing them as “typical American bullies”.

The agents claimed to be looking for undocumented immigrants, he said. Cook later said he had heard of 10 fishing boats being stopped by American agents in recent weeks.

After American fishermen came forward to say that their boats were also being intercepted by border patrol agents, the association said in a statement that they understood the incidents to be “part of a regular exercise being conducted along the US marine border”.

The reports come as relations between Canada and the US are at their lowest point in recent memory. After Donald Trump’s administration imposed tariffs on Canadian steel and aluminum, Canada – the world’s biggest consumer of American steel – launched retaliatory tariffs, plunging the longstanding allies into a trade war.

The tit-for-tat tariffs took effect weeks after the US president lashed out online at Justin Trudeau, calling the Canadian prime minister “meek and mild” on Twitter and accusing him of being dishonest.

The maritime boat checks risk now joining the list of irritants between the countries, after Ottawa said it was investigating the reports. “Canada’s sovereignty over the Machias Seal Island and the surrounding waters is longstanding and has a strong foundation in international law,” said a spokesperson for Global Affairs Canada.

The statement also noted the “long history of cooperation” between Canada and US in the area.

In a statement to the Guardian, US Customs and Border Protection confirmed that agents had “interviewed” 21 Canadian vessels so far this year. They declined to specify how many of these were fishing vessels.

The agency was conducting patrols to enforce immigration laws and other potential violations of federal law, the statement said, adding that among the Canadian vessels that were stopped, no immigration arrests were made.

The statement noted that agents based in Maine have “conducted operations in the past in this area and will continue to conduct operations in the waters off the coast of Maine in jurisdictional waters of the United States”.

Given the area, any focus on immigration would be surprising, said Stephen Kelly, a research scholar at Duke University and former American diplomat who served in Canada. “Because it’s not exactly what you would call a major people smuggling route, as far as I’m aware.”

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He speculated that the agency might have obtained intelligence on people being moved through the area or on other federal crimes such as drug smuggling.

He pointed to the ongoing territorial dispute to explain why the issue had made headlines, with initial media reports suggesting that US law enforcement had intercepted Canadian vessels in Canadian waters.

“I’m sure from the border patrol’s perspective, that’s not at all what they were doing,” he said, citing the American claim on the area that dates back to the late 1700s.

Kelly has long argued that the two countries should come together to resolve the dispute, rather than allowing it to fester and flare up now and again. “I don’t think its going to lead to blows between the US and Canada, although the current environment is not as rosy as it has been in the past,” he said. “But why let an issue like this hang out there and provide a burr under the saddle?”