Exclusive: two Sri Lankans who witnessed the violent final showdown of the country's 26-year civil war claim a top military commander and Sri Lanka's defence secretary ordered war crimes.

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Warning: You may find parts of this report distressing.

One of these eyewitnesses, an army officer, accuses Defence Secretary Gotabaya Rajapaksa - the president's brother - of ordering Brigadier Shavendra Silva to execute Tamil rebel leaders, whose safe surrender had been guaranteed by the president.

The other new witness, who was also operating with Brigadier Shavendra Silva's 58 Division on the front line during the final assault, claims the Brigadier was ordered by the defence secretary "to finish the job by whatever means necessary."

'Licence to kill'

He said this was interpreted by the soldiers as a licence to kill. He described how he had watched as Sri Lankan forces shot dead unarmed Tamil women and children. It is the first time this allegation has been made.

The war was won by Sri Lankan government soldiers two years ago. The rebel leadership was virtually wiped out.

They shot people at random. Stabbed people. Raped them. Cut out their tongues, cut women's breasts off. I saw people soaked in blood. - 'Fernando'

As the army closed in, around 130,000 Tamil civilians had been trapped on an ever-shrinking shard of land on the north-east of the island alongside the besieged rebel fighters, who are accused of using them as human shields.

The Sri Lankan president said no civilians were killed by the army during the final assault. But the United Nations now believes that up 40,000 civilians were killed during the last few weeks of the conflict. Others estimate the toll to be higher.

More from Channel 4 News: The Sri Lankan soldiers 'whose hearts turned to stone'

Most are thought to have died as a result of gun and mortar fire allegedly directed on them deliberately by government forces.

After repeated requests for an interview with Shavendra Silva - now retired and promoted to the rank of major-general - Channel 4 News went to confront him with these allegations in New York, where he serves as Sri Lanka's deputy ambassador to the UN.

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Former Sri Lankan President denounces current government
The latest revelations on Channel 4 News came after the former president of Sri Lanka condemned the current government in a speech in Colombo. Chandrika Kumaratunga warned that the country could descend into anarchy following the civil war between the govenment and Tamil rebels. Speaking in Colombo, Mrs Kumaratunga said her children had reacted with 'shock and horror' to Channel 4's 'Killing Fields' documentary which alleged war-time atrocities. "My 28 year-old son called me, sobbing on the phone to say how ashamed he was to call himself a Sinhalese and a Lankan," she said. Mrs Kumaratunga served as President of Sri Lanka from 1994 to 2005. She is the country's only female President to date.Kumaratunga suffered permanent nerve damage and lost vision in her right eye following an assassination attempt by the Tamil Tigers at her final election rally in Colombo in 1999.

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Allegations denied

Outside his embassy, the major-general denied allegations of war crimes and said such accusations stemmed from Tamil Tigers and their supporters.

He denied that soldiers under his command had raped or murdered civilians and he demanded we reveal the identity of the army officer who had alleged he had ordered the execution of surrendering rebels.

'Soaked in blood'

The allegations from the army officer serving with the then Brigadier Shavendra Silva surround what a recent UN report calls "The White Flag Incident" on the very last day of the war. Those killed included the Tamil Tigers' two most senior political leaders and their families.

Channel 4 News has identified their bodies among scores of dead insurgents in photographs of the aftermath provided by the officer himself. We are protecting his identity but he was interviewed in secret by a journalist working for Channel 4 News in Sri Lanka.

He told us: "We received orders from the top to kill some of those who surrendered. All regiments received the orders unofficially - from the top."

The officer continued: "The defence secretary phoned Brigadier Shavendra Silva and ordered him not to take them prisoner, but to kill them. When I got there, I saw a pile of dead bodies. This is the notorious 'White Flag Incident.'

"I can confidently state," he said, "that those who ordered the killings were Defence Secretary Gotabaya Rajapaksa and Brigadier Shavendra Silva."

The other new eyewitness, whom we've called 'Fernando', recounted apocalyptic horrors he had witnessed while with Brigadier Shavendra Silva's 58 Division. He accused Sri Lankan soldiers of war crimes which targeted civilians.

"They shot people at random. Stabbed people. Raped them. Cut out their tongues, cut women's breasts off. I have witnessed this with my own eyes."

'Fernando' continued as though in a trance, with tears running down his face: "I saw the naked dead bodies of women without heads and other parts of their bodies. I saw a lot of small, innocent children getting killed in large numbers. I saw people soaked in blood."

Asked if he had actually seen Sri Lankan soldiers shooting civilians, 'Fernando' said: "I saw them shooting. I saw it directly. I saw ordinary civilians getting killed with my own eyes."

Sri Lankan troops. (Getty)

'Finish the job'

This witness said the hearts of soldiers on the battlefront "turned to stone" as they carried out what lawyers told us could amount to war crimes and crimes against humanity.

He said that a few days before the end of the war, the brigadier had assembled his officer corps on a beach and told them he had received orders from the defence secretary "to finish the job by whatever means necessary."

He told me that we only have a small chunk of land left to capture. Do whatever it takes- finish it off the way it has to be done. - Witness 'Fernando'

'Fernando' relayed what the brigadier told his men: "He said: 'This is a very decisive day for us because last night I got a call from the defence secretary. He told me that we only have a small chunk of land left to capture. Do whatever it takes- finish it off the way it has to be done."

'Fernando' says that what followed was the killing spree he witnessed. "All they wanted," he said, "was for the war to be over."

Credible allegations of war crimes

In April, a panel of experts commissioned by the UN Secretary General to examine 'Accountability in Sri Lanka', found credible allegations of war crimes in Sri Lanka, committed by both sides.

These included the killing of civilians by shelling, the shelling of hospitals, the denial of humanitarian assistance and other human rights violations inside and outside the conflict zone.

The panel recommended that these allegations required further investigation.

The secretary-general is expected to present the experts' report to the UN Human Rights Council in Geneva. It will fall to the council to decide of the course of any further action.