"My government did not cooperate with this investigation for many reasons. Foremost of which was that it was instituted outside the established procedure of the UN Human Rights Council," Rajapaksa said.
"The usual procedure was for the President of the UNHRC to appoint a three-member independent panel to carry out the investigation after the relevant resolution is passed in the Council. However the investigation on Sri Lanka was not carried out by an independent Commission of Inquiry," he said.
Sri Lanka's Tamil minority say they lack trust in a local inquiry into the war, in which more than 100,000 people died.
President Maithripala Sirisena's new government, which in January came to power strongly backed by the Tamils, has vowed to punish war criminals of the conflict fought under the command of his predecessor, Rajapaksa, who ruled Sri Lanka for nearly 10 years.
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"Furthermore all the important staff positions in this body are held by Westerners who make up half the cadre of the OHCHR .... Given the composition of the OHCHR, it would not be possible to expect an impartial inquiry from them," he said.
"Neither the OHCHR nor the UNHRC has the authority to set up an international war crimes tribunal. The only body with the authority to do so is the UNSC where the veto power of China and Russia will be a factor to contend with," he said.
Rajapaksa's handling of the war has been internationally condemned for rights abuses. The UNHRC has passed three successive resolutions against his administration -- the last of which in 2014 recommended an international investigation.