Canada is investigating incidents of US patrol boats straying into waters it claims as its own and approaching Canadian fishing vessels.
A representative with the Grand Manan Fishermen's Association said US border agents tried to stop a Canadian vessel while looking for illegal immigrants.
The alleged incident happened on 24 June near Machias Seal Island.
The island is located between the Canadian province of New Brunswick and the US state of Maine.
It is the only contested territory between the two countries on the East Coast. The US and Canada have a long history of co-operation in the area on managing issues like fishing, though tensions have occasionally flared over the lobster-rich waters.
Laurence Cook, chairman of the fishermen's association, wrote on Facebook that the fisherman, Nick Brown, informed US Border Patrol Agents he was in a Canadian vessel legally fishing in Canadian waters. Mr Cook said the agents told him they were looking for illegal immigrants.
"Typical American bullies," he wrote in the June 25 post. "Proud of Nick not surprised to see the Americans trying to push people around."
Global Affairs confirmed that Canada is looking into "these incidents that occurred in Canadian waters, including through engaging with US agencies involved in the matter".
"Canada's sovereignty over the Machias Seal Island and the surrounding waters is long standing and has a strong foundation in international law," spokesman John Babcock said in an emailed statement.
The federal agency did not confirm how many vessels this had happened to.
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.
The organisation said they were told that US border agents approached Canadian fishing vessels as part "of a regular exercise being conducted along the US marine border".
The region is well-known for its lobster, as well as for herring and scallops.
A Customs and Border Protection spokeswoman told the BBC that US Border Patrol was "conducting regular patrol operation to enforce immigration laws and other violations of federal law that they may encounter in the course of their duties" during June.
The spokesperson said that border agents do not board Canadian vessels in the so-called "grey zone" around the island without consent or probable cause and only conduct interviews "as a vessel runs parallel to it, bow to stern".
She said there had been 21 Canadian vessels interviewed by agents in the sector so far this fiscal year "with no immigration arrests".
Tensions between Canada and the US are currently high over trade issues related to American tariffs on steel and aluminium and retaliatory Canadian levies; disputes over dairy, lumber, and wine; and the renegotiation of the North American Free Trade Agreement.
The Trump administration has enacted strict policies on illegal immigration in the United States, including a "zero tolerance policy" of criminally prosecuting anyone who crosses the border illegally.