The Defense Ministry officials say Monday's attack killed the deputy, Saudi national Saeed al-Shihri, as he left a house in the southern Hadramawt province.
They say the missile was believed to have been fired by a U.S. operated drone. The U.S. doesn't usually comment on such attacks but has used drones in the past to go after al-Qaida members in Yemen.
Al-Qaida's Yemen branch is seen as the world's most active, planning and carrying out attacks against targets in and outside U.S. territory.
The officials spoke on condition of anonymity because they were not authorized to speak to the media.