Maj. Gen. Ahmed Seif told The Associated Press that troops entered Zinjibar, the capital of Abyan province, and Jaar as al-Qaida militants fled into the mountains under heavy fire and airstrikes that killed more than 40 militants and destroyed several of their vehicles.
He said three soldiers were killed and two wounded. He spoke from the town of al-Husson, north of Jaar.
Military officials had earlier said that government forces entered the small town of al-Kawd after brief clashes.
Residents of al-Kawd said army trucks with loudspeakers urged them to stay inside until the town is fully liberated.
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Speaking on condition of anonymity for fear of retribution, the residents said two civilians were killed and four others wounded when a warplane bombed a car carrying explosives.
Al-Qaida seized both Zinjibar and Jaar last year, exploiting the chaos of Yemen's civil war, which pits an array of pro-government forces against Shiite Houthi rebels.
The militants agreed to withdraw from the towns in May but maintained a presence in the area.
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