The warrant for Maj. Gen. Ali Mamlouk, head of the Syrian National Security Bureau, was issued in absentia, with his address listed as "unknown," The (Beirut) Daily Star reported.
The case was referred to Military Prosecutor Saqr Saqr, who will make recommendations on the case before Mamlouk is given a military trial.
The indictment issued by Investigative Judge Riad Abu Ghayda against Mamlouk was also expected to include measures against the general's aide, judicial sources said. Those measures could include issuing a search warrant.
In August, Mamlouk, his aide and former Lebanese Information Minister Michel Samaha were accused by Judge Sami Nader, deputy commissioner at the military tribunal, of plotting to assassinate political and religious figures in Lebanon and carry out terrorist attacks.
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