The commission made that submission to the UN Human Rights Committee, which opened its review of Canada's compliance to the International Covenant on Political and Civil Rights on Monday.
There was broad criticism of the Harper government's policies on murdered or missing aboriginal women as well as Canada's approach to terrorism, including the recent passage of the anti-terrorism act.
It's the first time Canada has been examined by the panel since 2005, which makes this the first such examination of the Conservatives' rights record.
The Conservatives are no fans of UN oversight mechanisms, and have had some high-profile clashes with special rapporteurs on issues including relating to torture and aboriginal women.
The government will formally respond Tuesday to a variety of complaints at what is a regularly scheduled examination of Canada's record.
The review is taking place 100 days before the federal election, and could provide fodder for the government's domestic political opponents.
In its submission, the Canadian Human Rights Commission says the plight of aboriginal people is "one of the most pressing human rights issues facing Canada today."
It said that aboriginal people "continue to be significantly disadvantaged in terms of education, employment and access to basic needs such as water, food and housing."
The commission also said aboriginal women do not get equal access to justice in Canada.
"Indigenous women, in particular, bear a disproportionate burden of violence."
Similarly, the New York-based Human Rights Watch reiterated the findings of its 2013 report that criticized the RCMP for failing to protect aboriginal women in northern British Columbia.
The Canadian church-based group Kairos, which has had its funding cut by the Conservatives, asks the committee to "recommend changes in its policies and practices that would require Canada to take seriously its responsibilities to Indigenous peoples."
The federal government has rejected calls for a federal inquiry into the violence against aboriginal women, saying it supports provincial efforts in that regard.
Several groups also took aim at the government's recently enacted terrorism law, with Amnesty International calling on the committee to recommend that it be repealed because it does not impose adequate oversight on Canada's spy agency.
Amnesty also notes that the government still hasn't responded to the committee's 2005 recommendation for redress to three Canadian citizens — Abdullah Almalki, Ahmad Abou-Elmaati and Muayyed Nureddin — who were tortured in Syrian prisons.
And it wants the committee to urge similar redress to Omar Khadr after the Supreme Court of Canada's finding that Canadian officials violated his rights while he was in the U.S. military prison in Guantanamo Bay, Cuba.
"Whenever human rights have been violated, it threatens peace and security," said Sukanya Pillay, executive director of the Canadian Civil Liberties Association.
"Things like fundamental justice, due process, equality, all of these things have been on really shaky ground in Canada in recent years," she added.
"We are concerned that certain new legislation, while it might have been well-intended, has serious repercussions for civil liberties, and is at odds with Canada's legal commitments."
About two dozen groups, including the Canadian Human Rights Commission, Amnesty International and other civil society organizations were to give submissions to the committee on Monday and Tuesday.
Canadian diplomats in the Geneva, where the hearings are taking place, will present Canada's response starting on Tuesday. A Foreign Affairs spokeswoman said Monday that Canada is proud of its rights record, but did not elaborate on what diplomats would tell the committee.
The 18-member panel won't announce its findings for another two weeks. It is also examining the records of several other countries, including Britain, France, Spain, Macedonia and Uzbekistan.