A federal government wildlife committee recently concluded that their numbers near Cacouna have dwindled to 1,000 from a high of 10,000.
That information will make the project harder for TransCanada (TSX:TRP) to sell the Energy East project at environmental hearings in Quebec and with the National Energy Board, Couillard told a joint news conference with his Alberta counterpart, Jim Prentice.
"It's not my role to speak for the promoter or to answer for them but it strikes me it would be difficult to continue to see a port terminal at that site with that information," he said.
"Whether they want to choose an alternative site for the port is for them to decide but it certainly adds to the level of difficulty in view of the process that is going to start soon."
The Calgary-based company wants the terminal in Cacouna as part of its 4,600-kilometre pipeline, which would carry 1.1 million barrels per day of oilsands crude from Alberta to refineries in Quebec and New Brunswick.
On Monday, it announced it would halt all work on the terminal in response to concerns the project could hurt the beluga habitat.
TransCanada spokesman Tim Duboyce said the company will "review all viable options" after it analyzes the environmental report from the Committee on the Status of Endangered Wildlife in Canada.
Prentice, who is on a cross-country tour and will meet with Ontario Premier Kathleen Wynne on Wednesday, said his preferred option is for a terminal on the St. Lawrence.
"Clearly it's very difficult if the belugas, as an endangered species, are dependent on the Cacouna site," he told the news conference alongside Couillard.
"I hope there will be discussions between the proponents and Premier Couillard about other alternative locations. It would seem to me that the project will be stronger as a piece of nation-building infrastructure if there is a port facility in the province of Quebec."
Prentice reiterated the financial benefits he believes Energy East would bring.
"It's a very important project for the future of the country," he said. "It's important for economic growth in Alberta and for the entire country."
Late last month, Couillard and Wynne released a list of conditions for the pipeline to get the green light. They include emergency response measures, First Nation consultations and consideration of the impact on greenhouse gas emissions.
Prentice said he understands Quebec's various concerns.
"We share the same objective," said Prentice, who was elected in September.
"We want to see infrastructure in this country constructed in a safe way, in an environmentally responsible way. I think any province or proponent involved in the energy business has to be held to the highest possible standards."
On Monday, Prentice used a speech to a Vancouver business crowd to urge the country to get behind several controversial pipeline projects linked to Alberta's oilsands, warning that all Canadians will "feel the pain" if they aren't approved and built soon.