Vanniasingham Vigneswaran, who spearheaded the Tamil Resurgence Movement, a known front organisation of the rebel Liberation Tigers of Tamil Eelam (LTTE), was gunned down in the eastern town of Trincomalee, police said.
His movement had often clashed with the Sinhalese majority groups in Trincomalee where he opposed the erection of a Buddhist statue last year.
He had also led several strike actions in the area in support of the Tigers.
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Police in the multi-ethnic port town said investigations were at a very early stage and it was unclear who staged the attack.
The government issued a statement condemning the killing of Vigneswaran and President Mahinda Rajapakse sent police chief Chandra Fernando to visit the scene of the killing.
The government said it was "deeply concerned about politically motivated killings at a time when the Geneva talks are to begin in a few days".
The killing came as Norway's International Development Minister Erik Solheim and his deputy Jon Hanssen-Bauer lef