The government strongly rejects the allegations against it and the probe itself.
On Thursday, the UN Human Rights Council adopted a resolution co-sponsored by 41 countries, which allows the Office of the High Commissioner of Human Rights (OHCHR) to monitor progress and undertake a comprehensive investigation into atrocities committed in the months before the end of the war in May 2009.
Twenty-three countries voted in favour of the resolution, 12 against and 12 abstained from voting.
Pakistan proposed the removal of a key paragraph of the resolution which details the role of the OHCHR, but the council voted against its removal.
Ravinath Ariyasinghe, Sri Lanka’s UN envoy, “categorically and reservedly” rejected the resolution in a strongly worded statement, which did not address any of the allegations.
“The resolution will not only constitute a serious breach of international law but also sets a precedence on the sovereignty of nations,” said Ariyasinghe.
Speaking to Al Jazeera, spokesperson for Sri Lankan President Mahinda Rajapaksa, Mohan Samaranayake, did not say whether the government would cooperate with the investigation.
“Sri Lanka will study the entire process that has taken place so far … and will take appropriate action,” he said. “This is not about human rights, this is politically motivated, biased and [an] unjust infringement on the sovereignty of Sri Lanka.”
He said that entire moderate leadership had been eliminated by the LTTE during the 30 year war but that human rights had not been spoken about then.
“The government, under the leadership of President Mahinda Rajapaksa defeated terrorism and ensured the supreme human right, that is right to life.”
Navi Pillay, the UN High Commissioner for Human Rights, had recommended that the 47-nation council authorise the investigation, saying Sri Lanka has made “little progress” towards ensuring accountability for alleged atrocities and war crimes committed during the 26-year civil war against the Tamil fighters.
At least 100,000 people died during the war, which ended when government troops crushed the Tamil Tiger rebels who said they faced discrimination from the Sinhalese majority.
The vote required a simple majory from the council’s members.
An international investigation would allow witnesses to testify after domestic inquiries failed to carry out credible investigations, Pillay told the council in Geneva on Wednesday.
Sri Lanka, however, has rejected the US-led call for accountability and sternly rejected Pillay’s report, calling it biased, inaccurate and amounting to “needless interference” in the country’s affairs.
Sri Lankan UN envoy Aryasinha told the countries supporting the resolution not to “put spokes in the wheel” of the government’s reconciliation efforts before Thursday’s vote.
The UN, through two previous US-sponsored resolutions, urged Sri Lanka to implement the recommendations of a local panel appointed by President Mahinda Rajapaksa, which also urged punishment for soldiers involved in war crimes.
Pillay has said that the panel has not been effective or inspired confidence among victims and witnesses. The third resolution comes after Sri Lanka failed to implement the recommendations, amid continued alleged rights violations.
Sri Lanka has rejected any international probe.
Pillay concluded that democracy was being undermined and the rule of law was being eroded in Sri Lanka, with the country increasingly becoming an authoritarian state.
The US called on the council to investigate “past abuses and to examine more recent attacks on journalists, human rights defenders, and religious minorities”.
“There’s still much work to be done to ensure genuine reconciliation, justice and accountability for alleged war crimes as well as democratic governance and respect for human rights in Sri Lanka,” Paula Schriefer, a US deputy assistant secretary of state, told the council.
Before the resolution was passed, hundreds of protesters from Sri Lanka’s Thawheed Jamaath, a Muslim group, gathered in Colombo in opposition to the resolution on Wednesday.
“If the resolution passes, definitely the LTTE will try to reorganise and reestablish their power. If they reestablish their power, there will be another rise of war and rise of ethnic problems in Sri Lanka,” Thawseef Ahamed, one of the protest organisers, told Al Jazeera.
“We are now living a peaceful life and we don’t have any problems right now,” he added.
The UN and rights groups say that both sides are responsible for atrocities committed during the war but blame government troops for carrying out indiscriminate assaults on known civilian areas between September 2008 and May 2009.
A UN report found that as many as 40,000 people may have been killed in the final phase of the civil war, but the government disputes that figure.