The unknown assailants opened fire on Colonel Ahmed al-Suhaili, commander of a military camp in Hadramawt's city of Seiyun, the official said on condition of anonymity.
The defence ministry confirmed the attack on its website 26sept.net and said Suhaili responded by shooting at the assailants who were in a vehicle and wounded one of them before he died.
It said a search was on to hunt down the attackers but did not blame any particular group for the assault on Suhaili.
Members of Al-Qaeda in the Arabian Peninsula, the network's deadliest branch, frequently carry out hit-and-run attacks against intelligence and army officials, especially in the lawless south and east.
They generally use unregistered motorbikes to facilitate their escape.