Qassem Saadeddine said he received a call from the Islamic State of Iraq Thursday saying its members had killed Kamal Hamami, Iran's Press TV reported Friday.
Hamami, also known as Abu Bassel al-Ladkani, was killed after meeting members of the Islamic State of Iraq in Latakia to discuss battle plans, Saadeddine said.
Saadeddine said the rival militants threatened to kill all senior commanders.
In the past several months, rivalries and in-fighting have been on the rise among militants operating inside Syria.
The Free Syrian Army was formed in 2011 by army deserters based in Turkey and reportedly has about 40,000 members, the BBC said. Although somewhat successful in fighting against President Bashar Assad's forces, the rebel army says it cannot win the war unless it acquires more sophisticated weaponry.
In recent months, Western and Arab nations have agreed to increase support for moderate Syrian rebels.