General Abdel-Rahman al-Halili, commander of the first military district that includes the volatile Wadi Hadramout region, escaped unharmed when his convoy was hit during a field trip to his troops in the area, a regional official said.
Al Qaeda in the Arabian Peninsula (AQAP) exploited a power vacuum wrought by the 2011 uprising that eventually ousted President Ali Abdullah Saleh to carve out areas of dominance in south and east Yemen.
Since then, AQAP has repeatedly attacked state institutions, including army camps and state buildings across the US-allied country, killing hundreds of people.
Major powers are anxious to shore up the stability of Yemen, which shares a long, indistinct border with No. 1 world oil exporter Saudi Arabia, and whose coast gives onto major international shipping lanes.
The state news agency Saba said government forces had foiled three militant ambushes on the road from the Hadramout provincial capital al-Mukalla to Seiyoun in the Wadi Hadramout area - a distance of some 350 km (217 miles).
"The troops managed to eliminate more than nine terrorists and captured three," the agency said, adding that a number were also wounded while the rest fled.
The United States regards AQAP as one of the most active wings of the militant network founded by the late Osama bin Laden. Washington has stepped up its support for the government and military with drone strikes at the heart of its strategy.
Saba said Halili, the first district military commander, was on hand to greet troop reinforcements arriving in Seiyoun, but made no mention of the reported attack on his convoy.
In a separate incident, suspected al Qaeda rebels ambushed a military patrol in the Habban region in adjacent Shabwa province and killed two soldiers.
Militants have killed at least nine soldiers in separate attacks in south and eastern Yemen since last Saturday, local officials said, as the government began sending more troops to the east to confront the al Qaeda threat.
AQAP seeks to impose its radical version of Islamic law on parts of Wadi Hadramout where government control is perceived to be weakest. Residents said last month that leaflets had been distributed in Seiyoun warning women not to go out without being
accompanied by a man.
The militants dispersed into more remote areas of south and eastern Yemen in May after a military campaign drove them out of their main strongholds in Shabwa and Abyan provinces.
They have launched a series of attacks on government facilities in Hadramout over the past few months.