South Sudan President Salva Kiir sacked his powerful, hardline army chief Paul Malong on Tuesday, a government spokesman said.
General Paul Malong, long regarded as an ethnic nationalist of Kiir's majority Dinka tribe, was replaced by General James Ajongo Mawut, a career soldier.
"The decrees are two: one for the relief of Chief of General Staff, General Paul Malong Awan, and another decree is for the appointment of former Deputy Chief of General Staff for Administration and Finance General James Ajongo Mawut as the Chief of General Staff," Kiir's spokesmen Ateny Wek Ateny told AFP.
Ateny said the move was a routine changing of personnel. "This is a position that can be held between two years and four years and Malong has spent three years so this is the prerogative of the president" he said.
In February several senior army officers resigned, accusing Malong of conducting an ethnic war against non-Dinkas and ruling with an "unqualified clique of friends and relatives".
Among those who quit was Lieutenant-General Thomas Cirillo who has since announced plans to launch his own rebellion.
Malong is widely regarded as being the mastermind of fighting that erupted in the capital, Juba, last July killing hundreds and dashing hopes of a power-sharing government between Kiir and his former deputy turned rebel leader Riek Machar, a member of the Nuer tribe.
The Dinka and the Nuer are the two largest ethnic groups in South Sudan and have a history of bloody rivalry.
UN investigators were among those who blamed Malong for the bloody attacks in July in which civilians were killed and foreign aid workers raped.
The US subsequently failed to get Malong sanctioned and put on a UN blacklist, subject to an assets freeze and travel ban, for his role in the ongoing conflict.
South Sudan has been at war since December 2013 when Kiir fell out with Machar, accusing him of plotting a coup.
The conflict -- characterised by brutality and human rights violations -- has triggered famine in parts of the country, forced millions from their homes and killed tens of thousands so far.