"In a joint operation last night by the Somali national security and the United States, Al-Shabaab intelligence chief Abdishakur, also known as Tahlil, was eliminated," the Somalia National Security Agency said in a statement.
"Two other Al-Shabaab members also died in the attack," it added.
According to the statement, the joint operation was conducted in Saakow in Jubaland region some 320kms from capital Mogadishu
The Pentagon has confirmed launching an airstrike on a senior al-Shabaab leader in Saakow.
Tahlil headed Al-Shabaab's Amniyat unit which comprises the intelligence, suicide bombers and special operations.
The unit was reportedly responsible for the Christmas day attack on the largest military base of the African Union Mission in Somalia (AMISOM) where three peacekeepers and a civilian were killed.
Tahlil replaced Al-Shabaab intelligence chief Zakariya Hersi who was arrested over the weekend from his hideout near El Wak.
Hersi has since been handed over by the Somalis to Kenya.
Although the Somalia government did not identify the other two slain militants in the Monday's operation, a source in the Somali spy agency told The Anadolu Agency that they were top commanders Abu Muhsin Al-Ash’ari and Abdrahman Seylisi.
Al-Shabaab is yet to comment on report.
The group's leader Ahmed Godane was killed in a U.S. drone attack in Lower Shabelle in September.
Somalia has remained in the grip of on-again, off-again violence since the outbreak of civil war in 1991.
Earlier this year, fractious Somalia appeared to inch closer to stability after government troops and African Union forces – deployed in the country since 2007 – drove Al-Shabaab from most of its strongholds.