"Parliament is the forum for people's representatives. They will decide if the inquiry panel should be allowed into the country," he said while addressing a public gathering in the north central town of Medirigiriya yesterday.
Rajapaksa said his government had been penalised by the international community for ending terrorism.
"We have to go and file answers in Geneva every six months for the sin of liberating the country," he said.
His comments came as the UN rights chief Navy Pillay yesterday outlined her operationalising of the comprehensive investigation on Sri Lanka.
More From This Section
Lanka has repeatedly declined to cooperate with the investigation saying it was intrusive of its sovereignty.
Lanka's opposition was also stated by its UN Ambassador Ravinatha Aryasinha in Geneva yesterday at the opening of the UN rights body's 26th session.
Sri Lanka denies that its military killed any civilians, but instead says the defeated LTTE rebels.
The UN panel is said to be willing to visit Lanka between July and November.
Rajapaksa has two thirds majority in the 225-member parliament.