Major General Ubaya Medawela said the "unaltered" video suggested that what the documentary had presented as soldiers executing Tamil rebel prisoners actually showed rebels dressed in army fatigues.
The footage in the documentary, aired last month by Britain`s Channel 4, had an audio track with the soldiers speaking in the language of Sri Lanka`s Sinhala majority.
Medawela said the video the military had analysed had a Tamil soundtrack, suggesting the killers were rebels.
"The unaltered video received by the defence ministry provides ample evidence to prove the malicious intentions behind the doctored documentary of Channel 4," Medawela said.
The "original" version Medawela referred to was broadcast Monday by a pro-government Sri Lankan television channel.
Sri Lanka has persistently denied that there were any war crimes committed by its troops while battling the Liberation Tigers of Tamil Eelam (LTTE) rebels, who were crushed in an offensive that ended in May 2009.
It has has also accused Channel 4 and Western nations of leading a campaign to discredit its human rights record by producing reports of alleged war crimes and crimes against humanity.
In an email to the BBC, Channel 4 spokesperson Marion Bentley insisted that all the footage used in its documentary, entitled "Sri Lanka`s Killing Fields" had been found to be authentic.
She said it had been independently verified by experts in forensic pathology and video analysis and had twice been subjected to months of tests by audio-visual experts commissioned by the United Nations.
"We stand by this excellent journalism and do not accept that the footage we broadcast has been doctored in any way," Bentley said.
A Tamil politician said the soundtrack in the military-promoted version of the video was "suspect" and "unconvincing".
"The words don`t really fit the images," said the politician who asked not to be identified. (*)
Editor: Kunto Wibisono
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