In his letter to commissioner Yves Cote, Keith Stewart says Ethical Oil uses donations from individuals and corporations to finance ads attacking environmental groups opposed to the Northern Gateway Pipeline.
Stewart says the group's messages often mirror those of the Harper government.
He also says there have been a number of instances in which Conservative staff left government to work for Ethical Oil, then returned to political jobs.
Stewart says the organization draws on funding sources, such as corporations, not available to political parties, then spends money to support the Conservative agenda.
A spokesman for Prime Minister Stephen Harper says the allegations are ridiculous.
Stewart wants the elections overseer to look into possible collusion in the ties between Ethical Oil and the government.
The institute runs a website called ethicaloil.org which promotes support for the oilsands.
The website says it began as a blog created by Alykhan Velshi to promote ideas raised in Ezra Levant’s book Ethical Oil: The Case for Canada’s Oil Sands.
Greenpeace said Velshi was director of communications for then-immigration minister Jason Kenny before starting the blog and he later returned to work in the Prime Minister's office.
"The links between Ethical Oil and the Conservative party of Canada are clear," the Greenpeace letter said. "Ethical Oil's spokespeople, themselves Conservative party insiders and former staff, release specific messages that are repeated by ministers and even the prime minister is a fashion that appears co-ordinated."
Greenpeace said Ethical Oil does not disclose its sources of funding, but does say it accepts donations from Canadian individuals and companies.
"This indicates clearly that the organization receives corporate contributions."
The letter says if a third party raises money from sources which a political party cannot tap and uses it to support the party's agenda and if the third party was started by a member of the party with staff active in the party "then collusion has occurred."
Ethical Oil has complaints of its own about the environmental movement. It has asked the Canada Revenue Agency to investigate the David Suzuki Foundation and other green groups for engaging in partisan activity.