This is raising the prospect of further turmoil more than three years into an ethnically-charged civil war.
Kiir told reporters that Paul Malong had not obeyed orders to return from his home state to the capital to hand over to his replacement, and suggested unnamed foreigners were backing the general.
Kiir dismissed Malong – the man who has led his campaign against rebels – this week without spelling out his reasons. The general left Juba with a convoy of vehicles for Aweil in the northwest on Tuesday, raising speculation over his next move.
Several other senior officers have left the army in recent months, accusing the military of rights abuses and ethnic bias. One, Thomas Cirillo Swaka, has announced the formation of his own rebel force and threatened to topple Kiir.