Warning: Some may find the second image in the accompanying gallery distressing

New photographs have emerged which raise fresh questions about the conduct of Sri Lanka’s armed forces during the final stages of the operation against Tamil rebels and have led to claims the 12-year-old son of the militants’ leader may have been summarily executed.

A series of photographs taken a few hours apart and on the same camera, show Balachandran Prabhakaran, son of Villupillai Prabhakaran, head of the Liberation Tigers of Tamil Eelam (LTTE). One of them shows the boy sitting in a bunker, alive and unharmed, apparently in the custody of Sri Lankan troops. Another, a few hours later, shows the boy’s body lying on the ground, his chest pierced by bullets.

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The images were taken in May 2009 at the very end of the Sri Lankan government’s operation to crush the LTTE, which had launched a bloody, decades-long insurgency against the state that led to the deaths of perhaps 70,000 people. The authorities always said Prabhakaran’s son was killed in cross-fire, as troops moved in to take the LTTE’s last stronghold, located on a scrap of coastline near Mullaitivu in the north-east of the country.

But the images, contained in a new documentary, No Fire Zone, which will be screened at the Geneva Human Rights Film Festival during the UN Human Rights Council meeting in March, suggest the boy was captured alive and killed at a later stage.

A forensic pathologist who examined the later images for the film-makers, said the boy was shot five times in the chest. Furthermore, propellant burns around the wound suggest he was shot at very close range.

“The new photographs are enormously important evidentially because they appear to rule out any suggestion that Balachandran was killed in cross-fire or during a battle. They show he was held, and even given a snack, before being taken and executed in cold blood,” claimed the film’s director, Callum Macrae.

“It is difficult to imagine the psychology of an army in which the calculated execution of a child can be allowed with apparent impunity. That these events were also photographed and kept as war trophies by the perpetrators is even more disturbing.” The 12-year-old’s father, Prabhakaran, was killed along with most of the senior leadership of the LTTE as Sri Lanka’s army advanced on the rebels’ position. There were reports at the time that several LTTE officials were shot and killed as they tried to surrender.

Prabhakaran’s body was displayed on state television, part of the front of his skull missing, also suggesting he may have been shot at close range. The Sri Lankan authorities have always denied shooting anyone who was trying to surrender. Last night, Brigadier PR Wanigasooriya, an army spokesman, said Sri Lanka had been a repeated victim of “lies, half truths, rumours, and numerous forms of speculations”.

“No substantive evidence have been presented for us to launch an investigation,” he added, referring to alleged human rights abuses.

Sri Lanka has always insisted it did what it could to ensure no civilians were killed during its operation against the LTTE. Yet a team appointed by UN Secretary-General Ban Ki-moon found that up to 40,000 civilians may have been killed. The team said there were credible allegations both sides committed war crimes.

The photographs will place additional pressure on David Cameron to announce whether or not he will attend the Commonwealth Heads of Government meeting (CHOGM), e in Sri Lanka in November. A Downing Street official with Mr Cameron on his visit to India said on Monday that no decision had yet been taken.

NGOs and organisations, among them the cross-party Commons Foreign Affairs Committee, have called on him to boycott the meeting.

“The venue should be changed in light of the various stances and continuing violations in Sri Lanka,” said Maja Daruwala of the Commonwealth Human Rights Initiative. “We feel that the Commonwealth would lose credibility by holding the meeting in Sri Lanka.”

Edward Mortimer, chairman of the Sri Lanka Campaign, said: “Does David Cameron want to be part of the photo-opp for a kleptocratic and increasingly authoritarian leader with the blood of thousands on his hands? Will he advise the Queen to do so? I think we should be told.”