The claims are contained in a sworn deposition, seen by The Daily Telegraph, made by a career officer who rose to the rank of major general before he fled the country in fear of his life to seek asylum in the United States.
He is the highest ranking person to assert that atrocities against Tamil rebels and civilians were sanctioned at the highest echelons of the government. The source had the highest security clearance and close contact with some of the army’s most powerful figures.
His testimony contradicted a government-appointed commission, which concluded that Sri Lanka’s military did not intentionally target civilians.
The Lessons Learnt and Reconciliation Commission report, which was released last week, said some isolated allegations of civilian abuses by security forces needed to be investigated further, suggesting that any violations could only have resulted from soldiers who were not following orders.
That assertion flew in the face of an extensive United Nations report that accused the government of deliberately shelling civilian areas and possibly killing tens of thousands of people in the final months.
In his deposition, the major general says that he was informed that Gotabaya Rajapaksa, the defence secretary and brother of President Mahindra Rajapaksa, passed on “some instructions to a field commander to get rid of those LTTE [Tamil Tiger] cadres [who] are surrendering without adhering to normal procedures”.
Such an order, he said, “should come from either the secretary of the defence, with the knowledge of the president involved. He also has to be kept informed. The commanders could not undertake such decisions.”
It has been estimated that 20,000 people or more died in the closing months of the civil war in 2009.
The source, whose name has been withheld for his own safety, confirmed that assassinating Tamil Tigers who had been captured or surrendered became “standard operating procedure” as the Sri Lankan military forces closed in on the last rebel resistance on a strip of land on the island’s northeastern coast. Tamil activists are hoping that the evidence provided by the officer will build pressure for a war crimes prosecution against the president or defence secretary.
The US Department of Justice has a live file on the issue but has yet to prosecute, despite a leaked cable written by the US ambassador to Colombo which said that “responsibility for many alleged crimes rests with the country’s senior civilian and military leadership”, including both Rajapaksas and Gen Sarath Fonseka, then the armed forces commander.
American human rights lawyers are seeking to prosecute the defence secretary under the US Torture Victim Protection Act, which allows prosecutions against foreign leaders and officials who commit torture or extra-judicial killings.
Bruce Fein, a human rights lawyer, said that the alleged actions of Sri Lanka’s rulers and commanders appeared to be genocide.
“It’s hard to come to conclusion that the aim wasn’t to destroy the Tamil people in whole or substantial part,” he said, citing the definition of genocide under international law.
A video obtained by Channel 4 purported to show the assassination of what were thought to be Tamil rebels. The Sri Lankan army labelled the video as a fabrication. Other witnesses described various incidents of indiscriminate killing.
The UN also blamed the Liberation Tigers of Tamil Eelam (LTTE) for allegedly using civilians as human shields – a claim also made by the Sri Lankan government – and for using child soldiers.
Throughout its 26-year battle for autonomy, the ethnic minority rebels pioneered suicide bombing as a terror method, killed thousands of civilians among the Sinhalese majority and committed numerous atrocities that led to it being designated as a terrorist organisation by the US and Britain.
The testimony from the senior officer was first obtained by The International, an investigative website based in the US. It backed up various other allegations of illegal conduct by the authorities.
He said that to his knowledge shortly after becoming defence secretary in 2005 Mr Rajapaksa sanctioned the creation of a “hit squad” known for operating out of a white van to remove suspected LTTE members or collaborators off the streets of the capital Colombo.
Yolanda Foster, the Sri Lanka researcher for Amnesty International, said: “We doubt Sri Lanka’s will and ability to bring the perpetrators to justice, given the scale of the allegations and the potential that serving members of the Sri Lankan government may be implicated.”
A spokesman for the Sri Lankan high commission in London said: “We categorically deny these malicious allegations.”