Judge Sawan charged them with forming an armed organization, performing acts of terrorism, kidnapping people and terrorizing them by force of arms, and possession of unlicensed military weapons and ammunition.
He also referred them to the permanent military court for trial. Earlier this month, Military Investigative Judge Riyad Abu Ghayda issued an arrest warrant in absentia against 12 persons over their alleged involvement in clashes in the northern city of Tripoli, the latest round of which left at least 26 dead and 180 injured.
The port city of Tripoli has long been a stronghold of Sunni Islamists in northern Lebanon.
But the city has become increasingly volatile in recent months due to the civil war in neighboring Syria, where the Sunni majority is leading a revolt against President Bashar al-Assad.
Disputes from neighboring Syria's civil war frequently inflame sectarian grievances in Tripoli.
These clashes pit gunmen from both the mostly Sunni Bab al-Tabbaneh district and the Jabal Mohsen district which mostly comprises residents of Syrian President Bashar Assad's Alawite sect, a Shiite Islam offshoot.