In a statement, the ministry said that two men on a motorcycle shot Brigadier-General Abdullah al-Mehdar, a member of a committee restructuring the military, before fleeing, AP reported.
Local media said on Sunday that al-Mehdar was seriously injured last year in a bomb explosion, also in front of his home, and was flown to Jordan for treatment.
In a seperate development, a Yemeni security official told AP that a US drone hit several targets on Saturday in the province of al-Bayda, a stronghold of armed groups. The official did not give any further information.
Yemen's branch of al-Qaeda, also known as Al-Qaeda in the Arabian Peninsula, is seen by Washington as the most dangerous in the world and has been linked to several attempted attacks in the US.