The Tsleil-Waututh and Squamish nations have accused Ottawa of altering internal government documents related to the risks of marine spills before once again approving the Trans Mountain expansion project.

Details of these allegations were presented in the Federal Court of Appeal this week where four First Nations groups are challenging the re-approval of the pipeline, arguing that consultations with their communities once again fell short of the standard required.

A Federal Court of Appeal ruling in August 2018 quashed the initial approval of the pipeline expansion and forced the federal government to revisit the last stage of consultation with First Nations.

This week, the Tsleil-Waututh Nation, Squamish Nation, Coldwater Indian Band and a collective of Stó:lō bands are making their case about why they believe the renewed consultation efforts fell short in each of their specific communities.

The Crown-corporation-owned expansion project would twin an existing 1,150-kilometre pipeline that extends from Edmonton to Burnaby, B.C., nearly tripling its capacity to move oil from Alberta to coastal B.C., and then to markets in Asia. The cost has been estimated to be between $7.4 billion and $9.3 billion.

Tsleil-Waututh's core concerns about an expanded Trans Mountain pipeline are an increase in tanker traffic in the Burrard Inlet, impacts on the southern resident killer whale population and the risk of oil spills in the marine environment.

It says more research is needed on how to clean up a diluted bitumen spill and has concerns that it cannot be effectively cleaned up.

In 2018, Tsleil-Waututh commissioned three expert reports on these matters with the Squamish Nation. The nations, which have similar concerns about the project, submitted these reports to Canada during its reconsideration of the project.

In court on Monday, Tsleil-Waututh's lawyer accused Canada of suppressing internal documents related to these expert reports, saying they weren't handed over to Tsleil-Waututh until after the revisited consultations were complete.

"Canada belatedly gave [Tsleil-Waututh] a revised version of a scientific conclusion that was altered… to downplay the scientific consensus and instead advocate for a pro-approval position," lawyer Scott Smith told the court on Monday.

The Squamish Nation's lawyer Michelle Bradley raised similar concerns.

Speaking at a news conference on Monday, Tsleil-Waututh elected chief Leah George-Wilson said she was "extremely troubled" to learn about the allegations.

"The federal government initially denied the existence of its own peer review documents of Tsleil-Waututh and Squamish expert reports," she said.

In their argument about the reports being altered, Tsleil-Waututh's lawyer said after Canada re-approved the pipeline in June the nation came into possession of previous versions of Canada's internal reviews that showed the final version it got earlier had been altered to "support Canada's position and the ultimate outcome selected."

Tsleil-Waututh argued that previous versions of the reviews showed Canada's scientists agreed with the expert reports commissioned by Tsleil-Waututh and Squamish that found there is insufficient information on the behaviour of diluted bitumen to adequately address the risk of oil spill and clean up.

The Westridge Marine Terminal, the terminus of the Trans Mountain pipeline, is seen in an aerial photo over Burrard Inlet in Burnaby, B.C. in June. (Jason Redmond/REUTERS)

In its court filings Tsleil-Waututh details the alterations made in the five versions of Canada's internal reviews it obtained. It says it wasn't until later versions that the line "While not required prior to the GIC [cabinet] decision" was added to documents.

Tsleil-Waututh's legal team argued Canada was altering the reports to support its intention to re-approve the project and that this came at the expense of engaging in meaningful dialogue with the nation about its concerns.

This, Smith argued, is evidence of an "egregious" and fatal flaw in Canada's approach to the revisited consultation.

Canada calls allegations 'unfounded'

Canada's lawyers, who started their submissions on Tuesday, said the allegations were "unfounded" and that "there's nothing nefarious going on" in relation to the internal documents called into question or the behaviour of government officials.

They also objected to the characterization of the internal documents as peer reviews by government scientists. Canada described them as summary reviews used for the purpose of educating the consultation teams.

In their arguments, Canada's lawyers denied the government was suppressing materials and said sharing the drafts of the documents with Tsleil-Waututh illustrated their commitment to transparency. They also argued that any changes between versions of the documents did not reveal substantive changes.

They told the court that Canada engaged in reasonable consultation with both the Squamish and Tsleil-Waututh nations and that their applications to quash the approval of the project should be dismissed.

They also asked the court to discount the arguments put forth alleging document suppression and alteration in its assessment of the adequacy of consultation efforts.

Canada re-approved the twinning of the existing 1,150-kilometre pipeline from Edmonton to the B.C. coast in June after it revisited consultations with Indigenous communities as ordered by the Federal Court of Appeal ruling that quashed the government's initial approval of the project.

In opening submissions to the court on Tuesday, Canada's lawyers said the renewed phase three consultation was done reasonably, adequately and fairly and said the shortcomings identified in the previous Federal Court of Appeal ruling were not repeated this time around.

They pointed to the fact that Canada made amendments to project conditions as evidence of its responsiveness to the consultation process. They also pointed out that the revisited consultations were not applied just to the applicants in the Federal Court of Appeal case, but with all 129 Indigenous groups that stand to be affected by the project.

Canada's lawyers argued that all four applications in the court should be dismissed but asked that if the court sides with any or all of the First Nations on their allegations of inadequate consultation, the court not quash the entire project again. They argued it would be disproportionate to set aside the decision to re-approve the pipeline and instead proposed alternative remedies to the court to consider.

The hearings continue through Wednesday.