The official said on condition of anonymity that two armed men on a motorbike had opened fire on Lieutenant Colonel Mutei Baqatyan in the city of Mukalla on Saturday.
"He died instantly," the official added.
On December 18, the military intelligence chief of Yemen’s southeastern province of Hadramout, Colonel Mohammed Hadiq escaped an assassination attempt.
A week prior to the attack, masked gunmen on a motorcycle shot dead military intelligence officer Colonel Shakir Awad al-Bani near his house in the Hadramout province, killing him instantly.
Yemeni security forces frequently come under attack by gunmen especially in the southern and eastern parts of the country.