Paul Malong had been accused of directing fighting in the capital in July that left hundreds dead.
Ateny Wek Ateny told The Associated Press today that Malong was removed because he had been in charge for over three years. Ateny called that a violation of army rules.
The spokesman says Lt. Gen. James Ajongo Mawut has been named to replace Malong.
Malong did not answer repeated attempts for comment.
His removal comes after ethnic violence in South Sudan's civil war has dramatically increased. It also follows months of government infighting.