A breakaway faction of the rebel group, led by a former Tamil Tiger colonel, said it carried out Sunday’s killing of the commander who was known only as Ramanan.
Tamilnet, a pro-rebel Web site, confirmed Ramanan had been killed, but said he was "assassinated" by Sri Lankan army snipers.
Ramanan, a colonel in the rebel group, is one of the highest ranking Tamil Tiger leaders to be killed since a truce with government forces began in 2002.
The same day, suspected Tamil rebels attacked the offices of two international aid agencies and a foreign peace group, injuring a Serbian aid worker, the Sri Lankan army said.
In what is believed to be the first deliberate attack on foreign aid workers during continuing violence, grenades were thrown into three offices in the town of Mutur.
Two government soldiers were also killed in rebel attacks in the north and east of the country, the military said.
Daya Master, a rebel spokesman, said he was unaware of the attacks on foreign organisations, but added that "the LTTE [Liberation Tamil Tigers of Elam] would never attack NGOs and foreigners".
A spokesman for the breakaway group led by V. Muralitharan, better known as Colonel Karuna, said fighters had ambushed Ramanan as he drove by on his motorcycle, the AFP news agency reported.
They detonated a mine, which missed him, and then they opened fire on the rebel commander, killing him, the spokesman said.
The rebel movement split in 2004 when Karuna broke away with 6,000 fighters.
The Tigers accuse the government of supporting the group in its attacks on their fighters and allowing it to operate in its territory.
The rebels have fought the government since 1983, demanding a separate Tamil homeland.