Hundreds of people have been killed and thousands more terrified civilians have fled their homes to UN bases since Sunday.
The fighting, which has now spread outside the capital Juba, has raised fears in the international community of a return to civil war.
Kiir has accused soldiers loyal to fugitive former vice president Riek Machar of staging a coup attempt in the oil-rich but deeply impoverished nation, which has struggled with instability since becoming independent in 2011.
But Machar has denied any attempt to topple the president, and has instead accused Kiir of using the violence as a pretext to purge any challengers.
"What took place in Juba was a misunderstanding between presidential guards within their division, it was not a coup attempt," Machar told the Paris-based Sudan Tribune website Wednesday, his first public remarks since the fighting erupted.
"Kiir wanted to use the alleged coup attempt in order to get rid of us," said Machar, who was sacked by the president in July.
Kiir also said powerful military commander Peter Gadet -- who rebelled in 2011 but then rejoined the army -- had mutinied again, launching attacks in the eastern state of Jonglei in support of Machar.
In Juba, gunfire rang out into the early hours today, but by midday life on the streets showed signs of returning to normal.
But fighting was reported overnight yesterday in Jonglei's state capital Bor, with shooting breaking out again in the early hours of today.
The UN also reported clashes in the town of Torit, state capital of Eastern Equatoria.
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