The premiers of five Canadian provinces and one territory have warned Prime Minister Justin Trudeau's government that a pair of energy bills making their way through the federal legislature would shake investor confidence in the nation.

In a letter sent to Trudeau this week, the premiers urged him to take immediate action to "refine or eliminate" the bills or risk dividing the nation.

At the heart of the issue are bills C-69, which would change how natural resource projects including pipelines are assessed, and C-48, which would prohibit oil tanker traffic on the northern coast of British Columbia.

Both bills have cleared a third reading in the House of Commons, where Justin Trudeau's Liberals have a majority, and have been reviewed by the unelected Senate.

Bill C-69 was introduced by Trudeau's government in 2015 as part of a campaign pledge to streamline project assessments as well as restore stakeholder confidence in the system.

However, the legislation garnered more than 180 amendments in the Senate, making it more favourable to the oil and gas industry.

Amendments include measures to limit the authority of the environment minister to reject or approve major projects and to restrict the ability of groups opposed to fossil fuel development to testify at public hearings.

The bill has been sent back to the House to consider the amendments.

In their letter, the premiers urged the government to accept the full slate of changes, saying Bill C-69 as originally drafted would make it "virtually impossible to develop critical infrastructure".

Industry organisations, many of which lobbied for amendments themselves, also supported the changes.

"While this version of Bill C-69 is still not perfect, it is a significant improvement over the original version," Canadian Energy Pipelines Association chief executive Chris Bloomer said.

"With these amendments, we have a better chance of seeing new pipeline projects being proposed and built in the future."

The organisation submitted amendments, including ones to limit the discretion of the environment minister and to protect projects from judicial review and litigation.

However, environmental groups are worried the amendments would take the teeth out of the legislation's original mission to have authorities include climate impact while deciding on major projects.

"When Bill C-69 was first announced, many environmental groups supported the bill as an important step towards strengthening Canada’s broken environmental assessment framework," said Environmental Defence climate and energy programme manager Julia Levin.

"By introducing climate as a required consideration for projects, the bill ensured that approvals for future industrial projects would more closely align with Canada’s domestic and international climate commitments.

"However, the Senate committee reviewing the bill has put forth nearly 200 amendments, many of which would destroy the integrity of the bill in the interest of the oil and gas industry.

"If these components proceed as currently proposed we will have no choice but to withdraw our support from Bill C-69."

Meanwhile C-48 faces further debate in the Senate following its third reading. The bill advanced after a majority of Senators rejected a partisan committee report saying they should spike the legislation.

While the bill would enshrine in law what for years has been done as policy, the premiers said it would also prohibit major projects from being built.

"The tanker moratorium discriminates against western Canadian crude products," according to the letter.

"We would urge the government to stop pressing for the passage of this bill, which will have detrimental effects on national unity and for the Canadian economy as a whole."

However, British Columbia's government supports the tanker ban.

"We oppose the expansion of the movement of heavy oil through our coastal waters and we have been consistent in this position," the province's Minister of Environment & Climate Change Strategy George Heyman said.

"We acknowledge the measures included in the federal government’s Ocean Protection Plan. However, more investment is needed in marine oil spill preparedness and response along British Columbia’s coast to ensure that proven systems are in place to effectively respond to oil spills."

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Trudeau in trouble over energy bills