The officials told VOA's Somali service that Sheikh Hassan Dahir Aweys was taken into custody early Wednesday in the Himin and Heeb area.
Aweys led an alliance of groups that opposed the country's former U.N.-backed transitional government before merging with al-Shabab in 2010.
He recently fell out of favor with al-Shabab leadership amid disagreements over the group's strategy, after African Union and Somali forces drove the militants out of Mogadishu and other major cities.
Roland Marchal, a militancy and terrorism expert at the National Center for Scientific Research, says Aweys is one of the most prominent figures of political Islam in Somalia.
"In the Somali society this will be seen as a major victory against Shabab, no doubt," he said.
But he says he believes that within al-Shabab, Aweys will "mostly be seen as a traitor" and lose much of the appeal and respect he had in recent years.
The United Nations Security Council placed Aweys under sanctions last year. The council said his actions as a political and spiritual leader showed "an unequivocal and sustained intention to dismantle" the government and oppose the AU peacekeeping force AMISOM.
The United States designated him a terrorist in 2001, and further sanctioned him under an arms embargo in 2003.
A new Somali government, installed last year, is trying to bring order to a country that has endured more than 20 years of conflict and crisis.
AMISOM and Somali forces pushed al-Shabab out of Mogadishu nearly two years ago, but the group has continued to carry out periodic, guerilla-style attacks since then.