Constant gunfire and explosions in the early morning were followed by a few hours of relative calm before sporadic gunfire restarted, witnesses said.
Donald Booth, the US special envoy to Sudan and South Sudan, told the BBC: “The situation remains clearly tense and unsettled.”
The fighting has killed at least 26 people and exposed deep ethnic rifts in Africa’s youngest nation, which ceded from Sudan two years ago.
Kiir said on Monday that the fighting between army factions was a bid to seize power by Riek Machar, the former vice-president he sacked in July.
The two men, from opposing ethnic groups that have clashed in the past, have long been political rivals. Analysts said divisions run deeper and rivalries in army ranks have long simmered.
Poor communications in Juba, where the mobile phone system has not operated since yesterday evening, meant it was difficult to obtain a broad picture of the number of dead during the clashes, which have involved heavy arms and artillery.
Makur Matur Kariom, a doctor and Health Ministry official, told Reuters at least 26 people had died among the casualties brought to Juba Teaching Hospital, where he has been treating many of the wounded.
Residents near Juba airport, which has been closed since Monday, were woken before dawn by gunshots and blasts, a UN worker said. Others also reported bouts of shooting.
South Sudan’s government has struggled to create a functioning state since it declared independence from Sudan in 2011 after years of conflict with Khartoum during a war that often saw south-south clashes.
This week’s violence is the latest setback for one of Africa’s poorest states. Oil production, South Sudan’s main source of revenue, was shut down for 15 months until April because of a row with Sudan, which hosts the export pipeline.
Cutting off oil earnings and the flow of cash exacerbated tensions in a population of 11 million people desperate to see early benefits of independence, but who say the news state is plagued by old Sudan’s problems of corruption.
“Stopping the export of oil was a huge gamble,” said Cedric Barnes, Crisis Group project director for the Horn of Africa, based in Nairobi.
“That has put a lot of stress on the system as a whole. And the attempts at reconciliation within South Sudan have been politicized by all sides.”
Kiir and Machar have long been at loggerheads and their rival factions fought during the war with Sudan.
The president, who comes from South Sudan’s dominant Dinka ethnic group, sacked Machar, a Nuer, after mounting public frustration at the government’s failure to deliver tangible improvements in public services and other basic demands.
But analysts said tensions have been building in the army, broadly along those ethnic lines, but independently of the Kiir-Machar rivalry. They said a national reconciliation effort had faltered as officials were sidetracked by dealing with day-to-day problems of running a state with almost no revenues.
Politicians in the ruling SPLM political movement may now have limited sway over factions within the SPLA army that fought gun battles on Monday centered on two barracks to the north and south of Juba, analysts said.
“The personalities involved are clearly important, but we think this is more fundamentally about the SPLA rather than necessarily being completely controlled by the SPLM political figures,” Barnes said.
South Sudan is in desperate need of development. The size of France, it has barely any tarmac roads and citizens complain it suffers the same ills as old Sudan—corruption, poor public services and repression by the state of opponents and the media.
Kiir imposed a dusk-to-dawn curfew on Monday to try to restore order. Residents say the security clampdown makes life that was already tough harder still.
“Food and water is an issue for the population as they don’t have fridges or city power so they buy food almost daily,” said one aid worker in Juba, who asked not to be identified. “They haven’t stocked up and are getting worried.”
More than 10,000 civilians have sought refuge at two UN compounds in the city. Humanitarian agencies say they are unable to find out how many people have been killed or wounded as they are not allowed on the streets.