The national carrier “the move was necessitated by the uncertain security situation in the area” after 150 soldiers and dozens of civilians were killed in the renewed fighting.
The announcement came even as fighting between troops loyal to President Salva Kiir and those supporting his Vice President Riek Machar flared up.
The clashes broke out at a time when the oil-rich nation was marking its fifth year since independence and amid efforts to implement a ceasefire.
IGAD ministers were due to meet in Nairobi Monday to press the two leaders to stick to the peace accord that brought them together.
The violence in the world’s youngest country represents yet another blow to a shaky peace deal that has so far failed to end the civil war that broke out in December 2013.
The fresh fighting began when President Kiir and the rebel leader turned vice president Riek Machar met at the presidential palace and initially involved each of their bodyguards.
The ensuing shootout, lasting about half an hour, quickly escalated from rifle fire to heavier weapons, raising fears of high casualties as it spread with machine-gun bursts and artillery explosions heard in several parts of town.
A statement issued by South Sudan’s embassy in Washington said the exchange of fire between Kiir and Machar’s bodyguards followed an earlier deadly altercation that killed five soldiers at a checkpoint on Thursday night.
That incident left, “tensions running high and led to a misunderstanding”.