Sri Lanka's Tamil Tiger guerillas has a history of assassinating senior politicians in the island.
Minister Fernandopulle had been strong critic of the Tamil Tigers.
In January minister D M Dassanayake was killed by a blast on a road often taken by minister Fernandopulle, where he was widely believed to have been the target.
The Tamil Tigers have suffered several military reversal especially in the East of the country.
The assassination comes as the military is pushing towards guerrilla controlled areas in the northwestern Mannar area.