The Border Patrol operations came to light this week, when fishermen from New Brunswick's Grand Manan Island told news organizations they had been stopped in Canadian waters by U.S. Border Patrol and questioned about illegal immigrants.
Spokesman John Babcock said the Canadian government is also talking with US agencies, though he did not provide details about the fishermen's allegations or Ottawa's response.
A representative with the Grand Manan Fishermen's Association said USA border agents tried to stop a Canadian vessel while looking for illegal immigrants.
In a statement to the Guardian, US Customs and Border Protection confirmed that agents had "interviewed" 21 Canadian vessels so far this year.
Chair of Grand Manan Fishermen's Association, Lawrence Cook, said that over 10 fishing boats had been stopped for that reason.
Canadian officials are investigating reports about two vessels specifically, stopped on June 24 and 25, where American agents claimed to be "looking for illegal immigrants", according to the Canadian outlet CBC News.
He has argued that Canada and the USA should submit the disagreement to arbitration at the world court.
The patrols are part of recent increased enforcement actions nationwide by the USA agency, including a checkpoint last month along Interstate 95 north of Bangor.
According to Cohen, those seeking to cross the Canada-U.S. border illegally are usually pushing north.
The stops have been inconvenient, but he doesn't feel harassed, Drouin added.
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Despite their governments' debate, Canadian and American fishermen typically coexist in this area relatively peacefully - with a few notable exceptions.
Border Patrol has recently increased enforcement operations on major New England highways including a day-long roadblock on Interstate 95 near Lincoln in June and regular immigration checks of passengers at the Bangor bus station. USA law allows such immigration enforcement actions to be conducted anywhere within 100 miles of the border.
"There's been a bit of a misunderstanding there somewhere", Cook told the newspaper.
Machias Seal Island, which is about 19 kilometres southwest of Grand Manan Island and east of ME, is in a disputed area known as the Grey Zone, where lobster fishermen from both Canada and the United States have long fished side by side.
The State Department did not respond to a request for comment.
According to Cook, the Canadian fishing captain, Nick Brown, informed the USA vessel that "he was a Canadian vessel legally fishing in Canadian waters".
"Is this overkill? Absolutely".
"Until the matter of the boundary is resolved, we will continue to take practical steps with the U.S.to ensure that the area is well-managed".
Visitors head to Machias Seal Island on in June 2016.
The dispute has fueled tension between American and Canadian fishermen over the years, as the waters around the island are especially important lobstering grounds.
"I don't think you can draw a line between some of the concerns Americans have expressed for other border crossings with a fishing zone that has existed in the Bay of Fundy that has existed positively and collaboratively for a long time", he said.