Zakariye Ismail Hersi was captured in a raid Saturday morning in the town of El Wak near the border with Kenya.
General Abbas Ibrahim Gurey, the commander of Somali government troops in the southern Gedo region, told VOA's Somali service that authorities received a tip from members of the public that al-Shabab suspects were hiding in a house.
Gurey said that Hersi was captured with his secretary. The general said Hersi, who had a pistol on him, did not put up any resistance during the raid.
In June 2012, the U.S. put a $3 million reward for the capture of Hersi, describing him as an associate of former al-Shabab leader Ahmed Abdi Godane.
In an interview with VOA Saturday while in custody, Hersi himself confirmed that he was a member of al-Shabab. He said he left the group 18 months ago after differences with the leadership.
He said he was not aware if the U.S. had placed a bounty on him.
Hersi said he never became the intelligence chief of al-Shabab, as had earlier been reported. He said he held other positions, including head of Regional Administrations and was one of the commanders of al-Shabab militias.