One protester was killed in the riots which erupted after Aboud Rogo Mohammed was shot on Monday.
Youths from the port city’s large Muslim population took to the streets complaining he had been deliberately targeted by police.
Deputy police chief Robert Kitur said Rogo — who faced terrorism charges over allegations he was recruiting non-Somali Africans for Somalia’s al Shabaab group — was killed while driving in a private car.
In what police described as an act of impulse rather than a planned strategy to target Christians, protesters tried to burn two churches. Protesters also set alight a government vehicle.