"We have arrested around 250 members of Al-Qaeda, including some leaders, since our operations began," General Faraj Salmin told AFP.
Salmin commands the second military zone which includes Mukalla, capital of the vast desert province of Hadramawt.
The port city was retaken from the jihadists on April 24.
"One of these chiefs, Mohammed Saleh al-Orabi who calls himself the emir of Shar, was detained on Thursday" in the area of the same name some 60 kilometres (35 miles) east of Mukalla, he added.
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Al-Qaeda occupied the city for a year, and imposed strict Islamic law on residents.
Special forces from the UAE, a member of a Saudi-led coalition battling Shiite Huthi rebels across Yemen, played a major role in retaking Mukalla.
Last week, the United States said that "a very small number" of American soldiers were also involved in the operation.