"It's very difficult to identify the civilian casualties ... nobody talks of the LTTE's dead and injured," he said referring to the group's formal title, the Liberation Tigers of Tamil Eelam.
"They put all these figures also into the civilian casualty figure.''
The United Nations says at least 7,000 civilians were killed in the last five months of the conflict. In all, it says between 80,000 and 100,000 people were killed during the war.
The International Crisis Group reported earlier this year that at least 30,000 civilians could have died in the last years of the war. It also said civilians in the war zone were deprived of food and medical care.
Rights groups have called for an international probe into abuses by both sides, including allegations government troops shelled a "no-fire zone'' created by itself in the northeast of the island after hundreds of thousands of minority Tamils sought refuge there in the last stages of the fighting.
Rajapaksa told the commission that measures taken to prevent civilian casualties included restrictions on using heavy weapons, creation of no-fire zones, and sending convoys of food, medicine and other essentials.
Asked if Western governments or aid agencies raised questions of rights abuses by the army, Rajapaksa said: "No complaints about human rights violations or abuses by the army was brought to my notice. None at all."
He made no reference to relief agency reports of a "humanitarian catastrophe" during the final months of the war, including the killing of surrendering Tamil Tigers and shelling civilians.
He said the government has video proof to show Tamil combatants fighting in civilian
clothing and also using civilians for military work.
Sri Lanka's 25-year civil war ended in May 2009 after the government forces crushed the Tamil Tigers who had been fighting for an independent state for a quarter-century, after what they said were decades of discrimination of Tamils by the ethnic Sinhalese majority.
The eight-member panel is not empowered to probe war crimes, but is expected to focus on why a 2002 truce between the government and separatist Tamil Tiger fighters collapsed and led to more fighting.
Sri Lanka has rejected a separate UN probe into alleged rights abuses and resisted US-led calls for an independent international war crimes investigation.