In a decree read on national television this evening, Kiir also suspended Pagan Amum, the secretary general of the ruling political party, the SPLM.
Kiir also reduced the number of ministries in his government from 29 to 18, though it wasn't clear which ministries had been cut. No reasons were given for the shake-up.
Reports of a power struggle in the ruling party have persisted, particularly between Kiir and his first vice president, Riek Macher, who has said he is interested in running for president in 2015.
Last month, Kiir suspended two cabinet members and ordered an investigation into corruption allegations.