Five years after the Sri Lankan army crushed the remnants of a once-powerful rebel force, the United Nations is to launch a formal investigation into allegations that war crimes were committed by both sides.

In what campaigners said was a landmark decision, the UN Human Rights Council voted 23-12 in favour of launching the probe. The US and Britain had pushed for the resolution. India abstained in the final vote, while Pakistan accused those behind the proposal of hypocrisy and double standards.

The resolution adopted in Geneva calls on the UN’s senior human rights official to “undertake a comprehensive investigation into alleged serious violations and abuses of human rights and related crimes by both parties in Sri Lanka”. It calls for the probe to establish the facts “with a view to avoiding impunity”.

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Even before Sri Lanka’s operation to defeat the Liberation Tigers of Tamil Eelam (LTTE) was over, allegations of possible war crimes emerged from the battlefield and from civilian survivors held in detention centres.

The Tamil militants were accused of forced recruitment of children and the use of civilians as human shields. Meanwhile, the Sri Lankan military was accused of shelling so-called “no fire zones” set aside for civilians and shooting LTTE fighters who tried to surrender. Sri Lanka denied the allegations and insisted there had been no civilian casualties.

A three-strong panel established by UN secretary-general Ban Ki Moon, concluded in the summer of 2011 that there were credible allegations war crimes were committed in the final stages of the bitter, decades-long conflict.

The panel said that “tens of thousands” of civilians had lost their lives, and that most casualties were caused by government shelling. It said that in the aftermath of the conflict, the government of President Mahinda Rajapaksa had tried to intimidate the media and its critics.

Thursday’s decision was welcomed by human rights campaigners.

“The UN inquiry brings new hope for the thousands of victims of abuses in Sri Lanka,” said David Griffiths of Amnesty International. “The Sri Lankan government has twice ignored calls by the UN to conduct an independent and credible investigation... Now they have a fresh opportunity to restore some international credibility by cooperating with the investigation.”

Fred Carver of the London-based Sri Lanka Campaign said the UN High Commissioner for Human rights, Navi Pillay, now had the option of appointing independent investigators to assess the allegations or else carry out an inquiry herself.

“If Sri Lanka refuses access, then it will be an assessment of the information already available information,” he told The Independent. “Even if the Sri Lankans do allow access it will likely be stage-managed.”

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A succession of meetings of the UN human rights council have called on Sri Lanka to do more to investigate allegations of war crimes. Sri Lanka has repeatedly rejected calls for an independent probe and instead established its own inquiry, the Lessons Learned and Reconciliation Commission, which held a limited investigation and concluded that while the Sri Lankan army did not target civilians, the LTTE was responsible for abuses.

On Thursday, Sri Lanka rejected the UN resolution, saying it would be counter productive and insisting that it had already made measurable progress in addressing issues of accountability, according to the Reuters news agency.

“Sri Lanka categorically and unreservedly rejects this draft resolution as it challenges the sovereignty and independence of a member state of the UN,” Sri Lanka’s ambassador, Ravinatha Aryasinha, said in a speech before the vote was taken.

There were 12 abstentions among the 47-member council, including India, which had previously suggested it was planning to vote yes. Its representative told the meeting that Delhi believed adopting an intrusive approach would undermine “national sovereignty”.

Pakistan, which also has close ties with Sri Lanka, said the resolution was about politics and not human rights. “There is a dire need to comprehend and cooperatively address the enormous challenges being faced by Sri Lanka rather than penalising the country for rooting out terrorism from its soil,” said its envoy, Zamir Akram.

Tens of thousands of people lost their lives in the separatist insurgency launched by Tamil rebels in the north and east of Sri Lanka. Civilians, including school children, were often targeted by the LTTE.

Mr Rajapaksa and his bother, Gotabhaya, took the decision to root out the rebels and moved north to break through the front lines in the later part of 2008. By the spring of 2009, the rebels were holed up on a small patch of ground close to the ocean at Mullaitivu.

Reports from the battlefield said that makeshift clinics and a hospital were repeatedly shelled by the government troops, even though they were monitoring the area with drones. There have been other reports of extrajudicial killings and executions carried out by troops. All the allegations have been denied by Sri Lanka.

In the aftermath, Mr Rajapaksa, who was subsequently reelected president, was accused of launching a crackdown on his opponents and on the media.

Campaigners say such a crackdown is continuing. Amnesty said that in the last two weeks, three human rights activists had been detained and held on alleged suspicion terrorism. Among those held was activist Balendran Jeyakumari and her teenage daughter.