General Abdullah Mahmud al-Khalidi was shot dead on Monday evening in the northern Damascus neighborhood of Rukn al-Din, Syria's state television reported without providing further details.
Local media has blamed terrorist groups fighting against the Syrian government for the killing, adding that it was part of an insurgent campaign to target top figures and scientists.
Meanwhile, at least 25 insurgents were killed after members of two armed groups clashed in Aleppo suburb of Izaz on Tuesday over the distribution of goods they had stolen from locals.
There are also reports of clashes between government forces and foreign-backed insurgents in Hama, Dayr al-Zawr and Damascus suburbs. According to Syria's official news agency SANA, many insurgents were killed in Salah-Eddin and al-Khazan districts of Harasta in Damascus countryside.
Syrian troops also defused a number of explosive devices in Harasta.
Syria has been experiencing unrest since mid-March 2011. Many people, including large numbers of security forces, have been killed in the violence.