NISA in a statement said its cyber division had identified what it described as the virtual hubs for illicit activities by East Africa's al-Qaida affiliate.
The agency said it also disabled data services for approximately 2,500 phone numbers associated with them.
Somalia is seeking to disrupt al-Shabab's communication channels and financial transactions as part of a “total war” declared against the group that for years has controlled parts of the country and carried out attacks in the capital, Mogadishu.
African Union peacekeeping troops have been drawing down their presence in the Horn of Africa nation with the goal of handing over security responsibilities to Somali forces that have been waging the offensive declared by the president in 2022.