"The army intelligence command successfully arrested at dawn today a commander of the Abdallah Azzam Brigades, the wanted terrorist Jamal Daftardar, in a raid... In a village in the western Bekaa valley," an army statement said.
The military also said another group member, "who threatened to launch a hand grenade, was fired on and died on the spot".
The statement said the Daftardar's whereabouts were discovered in the course of an investigation "into the attack by a terrorist group against an army checkpoint in Sidon (southern Lebanon) on December 15".
An ensuing firefight killed four attackers.
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Daftardar was born in Tripoli, a majority Sunni city in northern Lebanon that sees frequent sectarian fighting related to the war in neighbouring Syria.
He is accused by the Lebanese judicial authorities of membership to "a gang whose aim is to commit crimes against people and financial interests, and to undermine the state's authority."
Daftardar is also accused of "possession of weapons and transporting explosive material, with a view to staging terrorist attacks," according to the text of an indictment issued in May 2008.
Daftardar's arrest comes days after the death in custody of Majid al-Majid, head of the Abdallah Azzam Brigades, which had claimed responsibility for a November attack against Iran's embassy in Beirut that killed 25 people.
Majid died of poor health, a judicial source said.
The group has also claimed responsibility for launching rockets against Israel.