The ministry statement said the raid took place on Saturday night in Abyan province in the town of Lawder, 155 miles southeast of the capital where government troops have for weeks been battling what it describes as Al Qaeda elements.
The statement added that further raids are planned in the area.
Elsewhere in south Yemen, gunmen from a separatist movement attacked an army post in Rabwa near the town of Habalein and killed four soldiers. Two of the attackers died as well.
Clashes between the military and separatists continued throughout the night, said officials on condition of anonymity because they were not authorized to speak to the media.
The south was once a separate country and simmering tensions there have compounded Yemen's troubles as it struggles with a resurgent Al Qaeda movement. Yemen is also the poorest country in the Arab world and home to heavily armed tribes that barely acknowledge the central government's authority.
The unrest in southern Yemen is separate from a six-year conflict in the country's north between government troops and Shiite rebels. That conflict appears to be drawing to a close since the two sides agreed to a cease-fire last month.
Southerners who joined a unified Yemeni 1990 have started a political movement demanding secession from the North, blaming the northerners for marginalizing them.
Al Qaeda has taken advantage of southern dissatisfaction with the government and established a presence in the remote region.