Lebanon's army has seized control of the headquarters of a radical Sunni sheikh whose supporters have battled the military for two days, killing 16 soldiers, an AFP correspondent at the scene said.

Sheikh Ahmad al-Assir's whereabouts are unknown, added the journalist, who accompanied troops into the complex in Abra, near the southern city of Sidon.

The correspondent saw abandoned weapons inside the cleric's headquarters, among them rocket launchers and machineguns, as well as military clothing.

Some of the flats in the complex were still burning as troops moved in.

The area sustained heavy damage in two days of fighting that broke out after Assir's supporters attacked a checkpoint, the army said.

The AFP journalist saw bodies on the ground, some of them scorched.

Troops said it was unsafe to remove them from the area for fear that they may have been booby-trapped.

Lebanon army to 'finish with' radical Sunni sheikh
Beirut (AFP) June 24, 2013 - Lebanon's army will fight until it "finishes with" a radical Sunni sheikh whose supporters have clashed with troops, killing 12 soldiers, the security cabinet said after a meeting on Monday.

"The army has a duty... to continue its operations until it finishes with the armed men, brings (Sheikh Ahmad al-Assir's) headquarters under control, and arrests the army's attackers," the statement said.

The statement comes after an emergency meeting, chaired by President Michel Sleiman, which included the commander of the Lebanese army, ministers and top security officials.

The meeting was convened to study "the progress of military operations after an attack on an army checkpoint" in Abra on the outskirts of the southern Lebanon city of Sidon on Sunday, the statement said.

Fierce clashes have raged in Abra since Sunday, leaving 12 troops dead, among them two officers, according to the army.

Five Assir supporters have also been killed in clashes near his headquarters in Abra, a source close to the cleric told AFP.

The army says the clashes broke out after Assir's supporters attacked a checkpoint in Abra.

Dozens of other people have been injured.

Assir was unknown just two years ago, but he gained prominence as the spillover into Lebanon from the conflict in neighbouring Syria has escalated.

Assir is radically opposed to powerful Lebanese Shiite movement Hezbollah, close ally of President Bashar al-Assad's regime.