The statement by Somalia's information minister said Lower Shabelle regional leader Moalin Osman Abdi Badil and three associates were killed Friday in Bariire village west of the capital, Mogadishu.
There is no immediate comment from the extremist group.
The raid came a day after a US service member was killed while supporting an operation by Somalia's military in the same area.
The Pentagon called it the first US combat death in Somalia since 1993. That's when US forces pulled out of the Horn of Africa nation in the wake of the "Black Hawk Down" incident in which two helicopters were shot down and bodies of American soldiers were dragged through the streets.
Somalia's new President Mohamed Abdullahi Mohamed on April 6 declared the country a war zone and launched a new offensive against al-Shabab, while offering the extremists a 60-day amnesty period to surrender.
"Leave al-Shabab now," the government statement said today. "Defect, as many of your brothers are beginning to do."
Somalia's military is under growing pressure to take full responsibility for the long-chaotic country's security as a multinational African Union force prepares to start withdrawing in 2018.
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