The "footage on the killings is nothing but lies," Rambukwella said in a statement. It added that the Al-Jazeera report was a collection of "bits and pieces" from a previous clip which the government dismissed as a fabrication.
Broadcaster Al-Jazeera said it had obtained the images from an unnamed Tamil source who said they had been taken by a member of Sri Lanka's military, which wiped out Tamil rebels in May last year.
Some of the disturbing photographs show bodies with twisted limbs piled on the back of a trailer, others show almost naked corpses, blindfolded and with hands bound behind their backs, lying in shallow graves.
Al-Jazeera said it was unable to verify their authenticity, adding that it was unknown if the bodies had been collected after a clean-up or were the result of a massacre.
The military onslaught against the Tamil Tiger rebel group has been dogged by allegations of war crimes, with the United Nations, Western powers and rights groups pushing for a probe of possible violations by both sides.
Other similar photos and video footage have emerged in the past.
In January, UN human rights envoy Philip Alston concluded that video footage said to be of Sri Lankan troops executing unarmed Tamil Tiger rebels was authentic and urged Colombo to accept a war crimes probe.Sri Lanka also dismissed this footage as fabricated.