Pillay's office must provide evidence to prove the allegations in order to investigate it, said government spokesman Keheliya Rambukwella.
Rambukwella, also the Minister of Information, told the Colombo Gazette that some groups may attempt to discredit the government by either threatening those who spoke to her or making false claims to that effect.
The minister also said the UN High Commissioner of Human Rights was given the freedom to travel and meet anyone she wanted and that opportunity may have been used by those who wanted to meet her and pass false information.
Meanwhile, the government downplayed any negative impact from the visit of Pillay.
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Pillay yesterday said unless Sri Lanka puts in place a credible investigation into alleged high number of disappearances and murders during the armed conflict "calls for an international inquiry are likely to continue".
Rambukwella said Sri Lanka as a sovereign state was within its right to decide on issues. "We have implemented most of the recommendations of the Lessons Learnt and Reconciliation Commission. So we have nothing to hide".
"There is nothing that so called powers can do. The US is indebted to China so no longer they are powerful to do us anything," Ranawaka said.
Pillay said she would be orally reporting to the UNHRC and in the process warned that Sri Lanka was "heading in an increasing authoritarian direction". She said despite the end to the armed conflict four years ago the democracy has been undermined and the rule of law eroded.
Sri Lanka ran a campaign of public castigation of the UN Rights Chief for her Tamil affinity albeit of South African origin.
She was accused of favouring the LTTE and working to target Sri Lanka on the dictates of the pro-LTTE diaspora.