Tuesday was designated a day of national mourning in Lebanon, as the search continued for Takfiri sheikh Ahmad al-Assir who was not found when troops entered the radical cleric’s complex in Abra, near the southern city of Sidon.
The deadly fighting erupted on Sunday on the outskirts of Sidon and intensified on Monday.
A military source in Sidon said the army found "dozens of bodies of armed men, wearing military fatigues with their weapons lying nearby,” AFP reported.
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.
Weapons, including rocket launchers and machine guns, lay abandoned inside the Takfiri 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.
UN chief Ban Ki-moon on Monday condemned the attacks on the Lebanese armed forces.
He appealed to Lebanon's armed forces to remain loyal to President Michel Suleiman in the face of tensions fuelled by the Syrian conflict.
Ban stressed "that all in Lebanon should fully respect the authority of the state", a UN spokesman said.
16 Lebanese troops were killed in the two-day battle with Takfiri gunmen, 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 on Monday that the army would fight until it "finishes with" Assir as a judge issued a warrant for his arrest.
The Takfiri sheikh had accused the army of siding with Lebanon’s resistance movement, Hezbollah.
He also encouraged his own followers to head to Syria to fight alongside militants against Syrian government forces.