S.P. Thamilselvan died with five others in an attack by the Sri Lankan air force on rebel-held territory, they said.
The defence ministry said it had targeted a venue where rebel leaders were meeting but gave no further details.
Thamilselvan had emerged as a de facto number two in the secretive Liberation Tigers of Tamil Eelam (LTTE), who have been fighting for autonomy for minority Tamils. The campaign has left tens of thousands dead since 1972.
He had led a peace-negotiating team at talks with the Sri Lankan government that were hosted by Switzerland last year.
But he had also been an active combatant who was injured while leading an offensive on an army camp in 1993.
He survived a 2002 bomb attack said to have been carried out by Sri Lankan security forces.
Thamilselvan acted as a de facto prime minister for the LTTE and was the public face of the group, which is led by the elusive Velupillai Prabhakaran, who is rarely seen in public.
"Head of our organisation's political