The ministry statement said the attack occurred today on the hospital in Hadramawt province, setting off a battle that lasted for an hour.
Yemen is home to one of the most active branches of al-Qaida group. The government has waged repeated offensives to drive out the militants from the south, most recently this spring.
The group retaliated with a series of attacks against troops and security. On Thursday, militants had carried out coordinated attacks against an airport, a military barracks and post office in the province, killing 15.
