Police have blamed the suicide bomb attack that killed Major General Parami Kulatunga and four other people, including the bomber, on the rebel Liberation Tigers of Tamil Eelam (LTTE).
Rajapakse said the killing showed the LTTE's "total disregard for the international community's repeated calls on it to cease all violence and acts of terrorism" and criticised the use of suicide bombers.
"These killings are further examples of the LTTE's concerted efforts to derail the peace process through acts of terror," the president said in a statement.
The bomber rammed the general's car as it made its way through early morning rush-hour traffic on a highway outside the capital Colombo.
Rajapakse last week sought to deal directly with the Tigers, asking for a two-week truce, but the rebels have made it clear they would not bypass peace broker Norway.
More than 60,000 people have died in three decades of ethnic warfare, as the Tigers try to carve out an independent homeland for nearly two million