Today was designated a day of national mourning in Lebanon, as the search continued for Sheikh Ahmad al-Assir who was not found when troops entered the complex in Abra, near the southern city of Sidon.
The deadly fighting, linked to rising sectarian tensions fanned by the conflict in neighbouring Syria, erupted on Sunday on the outskirts of Sidon and intensified yesterday.
An AFP journalist yesterday saw bodies on the ground, some of them scorched.
Troops said it was unsafe to remove them for fear they may have been booby-trapped.
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The army "has arrested dozens of people suspected of loyalty to Assir", the source added.
Ambulances took 94 wounded to hospital in the space of 24 hours, Red Cross operations chief Georges Kettani told AFP.
Weapons, including rocket launchers and machineguns, lay abandoned inside the cleric's headquarters, along with military uniforms.
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.
Virtually unknown until two years ago, Assir has capitalised on Sunni resentment against the Shiite Hezbollah movement's intervention alongside Syrian President Bashar al-Assad's forces against the mainly Sunni rebels.
Sixteen troops were killed in the two-day battle with his forces, among them two officers, the army said.
According to the army, the clashes erupted after Assir supporters attacked a checkpoint "for no reason".
A meeting of political, military and security chiefs pledged yesterday that the army would fight until it "finishes with" Assir as a military judge issued a warrant for his arrest.