Brigadier Balraj, a special commander of the Liberation Tigers of Tamil Eelam (LTTE), led the rebels' conventional fighting unit that has carried out repeated attacks on Sri Lankan troops.
The rebels did not give Balraj's real name or his age, but said they have declared three days of mourning, starting Wednesday.
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His death came as at least 12 Tamil Tiger rebels and three government soldiers died in renewed clashes in northern Sri Lanka.
The military said Tuesday that the fighting, which took place late Monday, was centered around the regions of Weli Oya, Janakapura, Andankulama and Kokkuthuduwal.
Military spokesman brigadier Udaya Nanayakkara said three policemen were also wounded when a grenade was thrown inside a police post in the northern district of Vavuniya on Tuesday.
Unidentified gunmen shot dead a paramilitary policeman while he was on duty in the southern town of Buttala late Monday, the defence ministry said.