The council approved a resolution, co-sponsored by Canada, which calls on the Sri Lankan government to fully examine allegations of summary executions, kidnappings and other atrocities by government forces and the Tamil Tiger rebels.
The resolution passed over the objection of the Sri Lankan government, which views it as an infringement of its sovereignty.
Foreign Affairs Minister John Baird said Canada continues to call for an independent investigation into alleged violations that occurred in May 2009 when government forces routed the Tigers to end the long civil war.
"Canada remains concerned that the government of Sri Lanka has not fully addressed the grave accusations of serious human rights violations that occurred toward the end of the conflict," Baird said in a statement.
"We continue to call for an independent investigation into the credible and serious allegations raised by the UN secretary general’s panel of experts on accountability in Sri Lanka that international humanitarian law and human rights were violated by both sides in the conflict.”
Baird said the resolution is a clear message to the Sri Lankan government to develop a plan, in conjunction with the UN rights body, that would implement recommendations of its own reconciliation commission’s report.
Human rights groups have accused the Sri Lankan government of using the commission to whitewash the matter.
"The resolution shows that the international community is sick and tired of the Sri Lankan government dragging its feet on accountability," Elaine Pearson, deputy director of the Asia division of Human Rights Watch, told The Canadian Press. "This resolution is an important first step towards justice for war crimes in Sri Lanka,"
Amnesty International said that if Sri Lanka fails to implement the resolution, the international community should be prepared to push for a full, independent inquiry.
Amnesty also took the Sri Lankan government to task for fostering hostility against the UN and human rights critics.
"They must end their campaign of intimidating peaceful critics and instead get on with the task of fulfilling the recommendations of their own national inquiry and their obligations under international law," Sam Zarifi, Amnesty's Asia-Pacific director, said in a statement.
Protests against the resolution continued in Sri Lanka on Thursday, with politicians, disabled soldiers and families of dead soldiers participating. Sri Lankan lawmakers also protested in Parliament and denounced the United States for taking the lead on the resolution.
Prime Minister Stephen Harper has said Canada will boycott the 2013 Commonwealth summit in Sri Lanka if the government does not take the war crimes issue more seriously.
Three Canadian parliamentarians are in Sri Lanka this week to evaluate the situation.
Parliamentary secretaries Chris Alexander and Rick Dykstra and new Sen. Vern White, the former Ottawa police chief, have planned a wide range of meetings with government and non-government officials throughout the country.
Ethnic Tamils in exile, including those in Canada's 300,000-strong diaspora, welcomed the vote as a first step toward accountability and peace in Sri Lanka.
"It puts the government of Sri Lanka on notice that the international community will no longer passively accept gross violations of human rights and humanitarian law," said Vani Selvarajah, a spokeswoman for Tamil organizations in Canada, Britain and the United States.
"Though we would have preferred the resolution to establish an international commission of inquiry, we see this as an incremental first step towards establishing a proper mechanism towards accountability in Sri Lanka."