It has also suspended two key Muslim civil society organizations for suspected Shebab links, which rights groups say will damage efforts to counter extremism.
Shebab insurgents from Somalia claimed responsibility for the April 2 attack on Garissa university in the east of the country which left nearly 150 people dead.
Since the attack, President Uhuru Kenyatta warned that the masterminds were "deeply embedded" inside Kenya, not just Somalia.
A $215,000 (200,000 euro) bounty has also been offered for alleged Shebab commander Mohamud, a former Kenyan teacher also known as "Kuno," who is believed to in Somalia.