The President's dismissal of the country's powerful army chief on Tuesday night has raised concern among the population.
President Salva Kiir's dismissal of Malong on Tuesday night has raised concern among the population who fear confrontation between soldiers loyal to each man.
Speaking at the presidential palace in Juba, Kiir presented Malong's dismissal as "routine work".
However, Kiir berated Malong who he said had erred by failing to thank him for the job he held and by not congratulating his successor, James Ajongo, on his new appointment.
"I was talking to him, I said, Malong, you did a mistake: the first thing that you should have done was to thank me personally for the period I have given you to serve the people of South Sudan. Secondly you are supposed to call James Ajongo and also congratulate him for his new assignment," Kiir said.
Kiir said that when he last spoke to Malong he was "in a fighting mood".
"I tried to calm him down but he was rather wild," said Kiir adding that the situation would be "contained".
Malong was due to return to the capital Juba later Friday.
The general is widely regarded as 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.