They show Balachandran Prabhakaran, son of rebel leader Velupillai Prabhakaran, eating chocolate on a bench.
Campaigning group Journalists for Democracy in Sri Lanka says they are proof the boy was summarily executed.
A military spokesman denied the allegations.
He said they were based on "lies, half-truths and rumours".
JDS says analysis of the photographs' metadata shows they were taken by the same camera at 10:14 and 12:01 on 19 May 2009 - on the final day of Sri Lankan forces' bitter 26-year war against the Tigers.
Velupillai Prabhakaran died at around the same time in a stretch of land between the Nanthikadal lagoon and the sea, where hundreds of thousands of civilians were trapped in the last bloody months of the conflict.
The army said he was killed in battle but human rights groups said he might have been killed after surrendering.
British film-maker Callum Macrae says the photographs of Balachandran Prabhakaran - which show the young boy first alert and unharmed and in the custody of soldiers but then dead, shot five times in the chest - rules out the government's assertion that Balachandran was killed in crossfire.
"His death was deliberate and calculated. This is a proof, beyond reasonable doubt, of the execution of a child - not a battlefield death," said Mr Macrae. "The pictures fill in chilling details on the circumstances of his murder - and leave the Sri Lankan government with yet more questions to answer."
But army spokesman Ruwan Wanigasuriya said the photos showed "no substantive evidence", and were being released in Mr Macrae's latest documentary, No Fire Zone (NFZ), that is timed to coincide with a session of the UN Human Rights Council next month.
In the past two years, Mr Macrae has made films for the British TV station, Channel 4, using video evidence to allege that the government side committed serious war crimes as it defeated the Tamil Tiger militants in 2009 - allegations always denied by Colombo.
The new film is set to be screened at the Geneva Human Rights Film Festival during a UN Human Rights Council meeting next month.
Meanwhile 133 Sri Lankan Christian clergy, mostly from the former war zone, have signed a letter urging the UN Human Rights Council to pass a strong resolution that is critical of Colombo and will set up an international inquiry into all alleged war crimes.
The mainly Tamil churchmen and women say that today the ethnic minority's culture, religions, language and land are being suppressed with what they say is "an intent to destroy us in whole or part".
Photographs have emerged which are said to show the 12-year-old son of a Tamil rebel leader alive and well in custody less than two hours before he was shot dead.