Interior Minister Abdikarin Hussein Guled told government radio that the Somali intelligence services have been tracking Ibrahim Ali Abdi, also known as Anta-Anta, for some time before the strike took place yesterday.
The minister did not say who carried out the attack, but an official in Washington said the US military carried out a drone strike targeting Shebab in Somalia yesterday.
"The operation in which this man has been killed was very important for the government. This man had a major role in the death of many innocent civilians and his death will help in bringing back peace," the minister told Radio Mogadishu.
There has been no comment from the rebels.
Also Read
The strike came weeks after an audacious attack on the Westgate Mall in Nairobi claimed by Shebab in which at least 67 people were killed.
It also follows a raid by US Navy SEALS on the southern port of Barawe in early October that failed to hit its alleged target: a senior Shebab militant leader and Kenyan of Somali origin called Abdulkadir Mohamed Abdulkadir, also known as Ikrima.
The source did not specify where the drone was launched, but the US army operates the devices from bases in Dijbouti and Arba Minch in southern Ethiopia.
The Shebab have been driven out of Somalia's major towns, including the capital Mogadishu and the key southern port of Kismayo, by a UN-mandated African Union force that now numbers 17,700 men.
However the group still controls large swathes of southern Somalia and has over the past few months stepped up the scale of its suicide attacks.