Military prosecutor Sakr Sakr arrested Ali Abdel-Wahad at the Beirut airport as he attempted to leave the country this month, The Daily Star reported.
Abdel-Wahad protected Sheik Ahmad Assir, a Salafist imam wanted by Lebanese officials to face charges of attempted murder, destruction and inciting sectarian violence. He and dozens of his supporters are also charged with forming an armed gang that intended to commit crimes against people and property, judicial officials said.
At least 18 soldiers and 28 of Assir's gunmen were killed last month in clashes at a checkpoint.
Two other Assir bodyguards who were charged, one Lebanese and the other Palestinian, were at large officials said.