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.
Chris Mills, a former lightkeeper in the Canadian coast guard, said he never saw a Border Patrol boat or a USA military vessel pass by when he worked at the Machias Seal Island Lighthouse in 1991 and 1992.
The waters that surround the island, at the mouth of the Bay of Fundy, in the Gulf of ME are also disputed.
"Canada's sovereignty over the Machias Seal Island and the surrounding waters is long-standing and has a strong foundation in worldwide law", said Global Affairs spokeswoman Elizabeth Reid, adding that Ottawa was reaching out to the USA authorities for more details on the incident.
A U.S. customs spokesperson said the operation, which is being conducted by the agency's Houlton, Maine, office, is part of a routine enforcement effort and such inspections have been made in the past.
US Border Patrol agents have been stopping and questioning Canadian fishermen in disputed waters about unauthorized immigrants.
U.S. Customs and Border Protection has not responded to a CBS News request for comment.
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"Houlton Sector Border Patrol has conducted operations in the past in this area and will continue to conduct operations in the waters off the Coast of ME in jurisdictional waters of the United States", Stephanie Malin wrote in an email.
"Canada's sovereignty over the area is long-standing and has a strong foundation in global law", the post said.
A spokesperson for the fishermen told the Press that agents boarded the boats asking about the presence of undocumented immigrants.
There's no telling just how American policing of the waters in the Gulf of ME will affect the Canadian fishing industry there.
The patrols are part of recent increased enforcement actions nationwide by the US agency, including a checkpoint last month along Interstate 95 north of Bangor. Machias Seal Island is located 16 kilometres southeast from Cutler, Maine, while 19 kilometres southwest of Southwest Head on Grand Manan Island in the Bay of Fundy. They declined to specify how many of these were fishing vessels.
But the United States has never relinquished its claim on the island.
On 4 July, the Grand Manan Fishermen's Association released a statement saying that both Americans and Canadians have jointly fished the 165 sq km (63 sq mile) area surrounding the island for years and have a "respectful and cordial" relationship.
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Like previously stated the island is in a grey area of the border but both Canadian and American fishermen work around the island.
Drouin said the area has been "inundated" with Canadian lobster fishermen since 2002.
"A lot of people are a lot more anxious about U.S. power on Canadian soil or in Canadian waterways", she said.
In 40 years fishing off ME, this is the first time he can remember Border Patrol operating offshore like this, Drouin said.
Drouin said he believed Canadians were overreacting to the Border Patrol stops. "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".
Machias Seal Island lies between a grey area in the Canadian and American border which the United States of America has recently begun monitoring more closely.
"It's a pretty significant area", said Geoff Irvine, executive director of the Lobster Council of Canada.
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We will see what happens and I will not - and don't want to - say it looks a little bit better in that department or this department.