Rajapaksa's office said Pillay expressed happiness over the post-conflict progress achieved by Sri Lanka. "It was very very visible to me in the North how you have invested in reconstruction," a presidential release quoted the UN Human Rights Commissioner as saying.
Rajapaksa told Pillay that there was a belief among many Sri Lankans that the UN is biased in the way it deals with countries.
Pillay's week-long visit has come under stiff protest from within government ranks. A section of the cabinet has dubbed Pillay an agent of the West which is out to undermine Sri Lanka as a nation.
Prior to meeting Rajapaksa, Pillay, a South African national of Indian Tamil origin, met with the country's main Tamil party TNA.
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"We drew her attention to the joint declaration between President Rajapaksa and UN Secretary General Ban Ki Moon," M A Sumanthiran, a senior TNA leader, said.
"All these should have been implemented within six months (of end to the conflict in 2009)", Sumanthiran said.
She also called on leader of opposition Ranil Wickremesinghe.
She also visited former conflict zones in North and East to get firsthand information that will be presented during the next sessions of the UNHRC in September.
Pillay's visit came following two successive UNHRC resolutions on Sri Lanka moved by US and backed by India. Both resolutions urged the country for expeditious implementation of the Lesson Learnt and Reconciliation Commission's recommendations for reconciliation with the Tamil minority.