Weerawansa also accused Pillay of holding secret meetings with activist groups outside of her official schedule and receiving "forged documents and faked photos."
Pillay's spokesman Rupert Colville said the rights chief was conducting the mission as she would in any country.
Pillay is to present her findings to the U.N. Human Rights Council next month. The council passed a resolution in March urging Sri Lanka to more thoroughly investigate alleged war crimes committed by government soldiers and the rebels. It also called on Pillay's office to orally report on Sri Lanka's progress in September and submit a detailed report next March.
Government troops defeated the Tamil Tigers in May 2009, ending their attempt to create a separate state for Tamils. A U.N. report said government troops may have killed 40,000 Tamil civilians in the final phase of the war.
On Tuesday, Pillay visited Mullivaikkal village in northern Sri Lanka, the site of the final battle of the civil war, where hundreds of civilians are alleged to have died. War survivors there complained to Pillay about missing relatives, military land grabs and a life without basic facilities more than four years after the war's end.
Many civilians and rebels said to have surrendered to the military toward the end of the fighting are reported missing.
The rebels are accused of killing civilians, using them as human shields and recruiting child soldiers.
Human rights groups say the military has seized about 6,400 acres (2,589 hectares) of land from war victims since the end of the fighting and now runs farms on the land.
Also Thursday, Pillay met with government officials, including Human Rights Minister Mahinda Samarasinghe.