"If there is evidence, it can be brought to the notice of the established Sri Lankan judicial system," Rajapakse told the Sinhalese-language Lankadeepa newspaper.
"They can even go through lawyers and inform the police."
Sri Lanka has consistently resisted international calls to probe allegations that thousands of Tamil civilians were killed during the final months of fighting against the Tamil Tiger rebels last year.
"I challenge them to produce evidence (of war crimes).
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There is no point in giving photographs and videos to the media. We have an established legal system.
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Use it," Rajapakse added.
His remarks came ahead of visit to the island by UN chief Ban Ki-moon's top political adviser, Lynn Pascoe, and a top Japanese envoy, Yasushi Akashi.
Both envoys are expected to push Sri Lanka to swiftly move towar