"President (Mahinda Rajapaksa) has directed his secretary Lalith Weeratunga to set up the committee," spokesman Mohan Samaranayake said.
Weeratunga would name the individuals who will form the committee as well as its terms of reference, Samaranayake said.
The committee will probe the entire period of 30 years when the LTTE was carrying out its separatist campaign, Samaranayake added.
Hundreds of people are still missing four years after the end of the war to defeat Tamil separatists in Sri Lanka. Most of the missing are Tamils.
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A government census carried out at the end of the war found 6,350 people missing in the north.
Human Rights groups had urged investigations in to the large numbers of disappearances blamed both on the LTTE and the government troops.
The UN in March asked Sri Lanka in a US-sponsored resolution to carry out credible investigations into killings and disappearances.
The government said its census results in the north pointed to rights groups' figures of the disappearance were gross exaggerations.