"There is a perception in the country about the lack of objectivity and fairness in the treatment meted out to Sri Lanka," G L Peiris told Pillay, who is here on a week-long visit.
He dismissed as unjustified the attempt to single out Sri Lanka for unfair treatment, after the country has been at the receiving end of two UN Human Rights Council resolutions.
"There has been prejudgement and we are disappointed," Peiris told Pillay who arrived here on Sunday for her first official visit after the government dropped its public hostility to her and promised access to the former war zones.
On the aspect of accountability which is a prime concern for Pillay, Peiris highlighted the action taken by the government.
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He cited examples of some members of the Special Task Force having been indicted in relation to the killing of five students in Trincomalee and status of investigations with regard to the incident involving French humanitarian workers.
Colombo is under pressure from Canada for a boycott of a Commonwealth summit here in November over alleged war crimes committed by the army during the final months of nearly three decades long conflict, which ended in 2009.
A South African national of Indian Tamil origin, Pillay is expected to record Sri Lanka's human rights accountability and progress in reconciliation. She will provide a first hand assessment on Sri Lanka at the next month UNHRC's session.
"She broke protocol, gave the slip to her security detail and went for secret meetings in Trincomalee to conspire against the country," Weerawansa told reporters here.
Pillay's visit came following two successive UNHRC resolutions on Sri Lanka moved by US and backed by India. Both resolutions urged Sri Lanka for expeditious implementation of the Lesson Learnt and Reconciliation Commission's recommendations for reconciliation with the Tamil minority.
As many as 40,000 people were reportedly killed in the last months of the conflict between Sri Lankan troops and the LTTE rebels fighting for an independent homeland.