According to the UN figures, up to 40,000 civilians were killed by the security forces during former president Mahinda Rajapaksa's regime that brought an end to the brutal conflict with the defeat of the Liberation Tigers of Tamil Eelamin 2009.
The LTTE ran a nearly three-decade separatist campaign leading to a bloody war with the Sri Lankan security forces.
Sirisena had earlier vowed to defend the troops against warcrimes charges leveled against them.
"You know that investigations are underway into a small number of officers who acted at the behest of politicians. Those who are in custody will be freed if they are innocent.
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"I hear allegations from (opposition) political stages that this is a witch-hunt of war heroes. I strongly reject those allegations," he said, adding that the military should clear its name.
Since Rajapaksa's defeat, several incidents of military excesses have come to be highlighted with several military men under arrest and later given bail as part of the proceedings.
During the Rajapaksa's regime, the soldiers were prevented from facing the legal process and the UN's call for independent investigations were dubbed as attacks against Sri Lanka's sovereignty.