The NEB has also made 16 new recommendations to the Governor in Council.
The recommendations include making changes to decrease underwater noise out of concern for the whale population, as well as recommendations on reducing emissions from vessels.
The decision was announced Friday morning in Calgary.
The energy regulator says an increase in tanker traffic resulting from the pipeline would hurt southern resident killer whales and increase greenhouse gas emissions.
But it says the side effects can be justified in light of the “considerable benefits” of the project.
“While these effects weighed heavily in the NEB’s consideration of project-related marine shipping, the NEB recommends that the government of Canada find that they can be justified in the circumstances, in light of the considerable benefits of the project and measures to minimize the effects,” said Robert Steedman, chief environment officer with the NEB.
WATCH BELOW: NEB reconsideration report says killer whales will likely be impacted
According to Steedman, the effect on the Salish Seas — a series of waterways in southwestern B.C. — and the marine life that lives in the area could be significant, but the area has already been highly disturbed and degraded by human activity.
“So the conditions in the Salish Sea are already detrimental to the species in question here, particularity the southern resident killer whale, so the panel concluded that even the relatively minor incremental effects of project related marine shipping must also found to be significant.”
The 16 new recommendations are designed to offset the impact on marine life, Steedman said.
The decision starts the clock on a 90-day deadline for cabinet to decide whether the project should proceed, but there have already been signals that the deadline could be pushed back.
Sohi’s spokeswoman wouldn’t comment on Thursday whether a cabinet ruling would be delayed.
In a statement issued after the announcement Friday morning, Sohi made no mention of the deadline for cabinet.
“We know how important this process is to Canadians,” he said.
“Moving forward, the Governor in Council will make a decision on TMX once we are satisfied that the Crown has adequately fulfilled its duty to consult. We are hopeful the work we are doing will put us in a strong position to make a decision within the NEB’s legislated timeframe.”
LISTEN BELOW: Minister Amarjeet Sohi speaks with Ryan Jespersen on 630 CHED
Sohi also thanked the NEB for their “timely work” and said the government looks forward to reviewing the report.
Alberta has been fighting hard for the Trans Mountain expansion so that the province could move more crude oil to ports and from there to lucrative overseas markets.
The consultations were also an issue the federal Appeal Court raised when it put a halt on the project.
The NEB was directed by the federal government to reconsider two aspects of the project recommendation report related to marine shipping in September of last year.
Former Supreme Court justice Frank Iacobucci was appointed to oversee a new round of consultations with Indigenous communities.
WATCH BELOW: West Coast Environmental Law opposes NEB’s latest decision
Opponents of the project are already planning their response, which will include legal challenges, said Sven Biggs, climate campaigner for Stand.earth, on Thursday.
“It’s likely there are going to be more lawsuits and more delays because of them, and if the cabinet decides to go ahead and restart construction, you’ll see protests in the streets and along the pipeline route,” Biggs said.
The project — which would triple the capacity of the existing pipeline between Edmonton and Burnaby, B.C. — has been in limbo while the federal government attempts to fulfill the Supreme Court’s requirements to consult Indigenous communities and consider the possible environmental impact of the additional oil tankers that would be off the coast if the project goes through.
The report was released on the deadline date set out by the federal government.
—With files from Dan Healing, The Canadian Press