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Qila, a Beluga at the Vancouver Aquarium is prepared for an ultrasound on April 14, 2014. The Ultrasounds are used in both animal care and research.John Lehmann/The Globe and Mail

Marine scientists in Quebec are raising alarms that TransCanada Corp.'s proposed Energy East pipeline project will threaten falling beluga populations in the St. Lawrence River.

TransCanada is conducting seismic activity near Cacouna, Que., on the south shore of the St. Lawrence River across from the mouth of the Saguenay River. Belugas are believed to calve in the Cacouna area in the late spring and early summer.

Three leading marine researchers wrote a letter this week to Fisheries Minister Gail Shea, complaining that seismic activity and other planned work pose a serious threat to the St. Lawrence belugas.

"We feel this area is an area of great importance to the population," Stéphane Lair, a professor of veterinary medicine at the University of Montreal, said in an interview Friday.

"Our concern now is that we know that belugas are sensitive to noise and we are concerned that all the construction activities that are going to be associated with that project will have an impact on these females … The population has been in really bad shape and this could be the end."

The number of belugas in the St. Lawrence is estimated to have declined from 1,100 to 900 over the past decade, and scientists are still trying to determine the cause.

TransCanada is proposing to construct a marine terminal in Cacouna as part of its $12-billion Energy East pipeline project to ship western Canadian crude to eastern refineries in Quebec and New Brunswick, along with export facilities in both provinces.

The Energy East project has been endorsed by Prime Minister Stephen Harper, whose government is eager to find alternatives to TransCanada's long-stalled Keystone XL pipeline, which would carry oil-sands bitumen to the U.S. Gulf Coast.

TransCanada expects to file an application on the pipeline with the National Energy Board this summer, and will apply to the provincial regulator for a permit for the Cacouna export terminal.

The company has permits to conduct seismic activity in April and drilling later in the spring to assess the nature of the seabed for the purposes of future construction, spokesman Philippe Cannon said. The seismic work will be completed by the end of the month to avoid interfering with the belugas' calving.

TransCanada has an "enviable safety record" and "will always obtain all necessary permits and authorizations before proceeding with any kind of work," he said.

Melanie Carkner, spokeswoman for the Department of Fisheries and Oceans, confirmed the department will allow the company to drill for core samples later this spring. "We're of the view that the proposal won't result in any harm," she said.

The beluga population is currently listed as threatened but the researchers say the work has been done to increase that threat to "endangered," a move that would require a more aggressive federal plan to protect them.

"It doesn't have the full protection it deserves; it should have been designated 18 months ago," Robert Michaud, a biologist at the non-profit Group for Research and Education on Marine Mammals, said in an interview.

Mr. Michaud said he worries that "political or industrial pressure" could interfere with the decision.

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