The violence was the focus of an emergency UN Security Council meeting, which heard that as many as 800 people had been injured, and some 20,000 people had sought refuge in UN compounds.
“UN officials have told me they’re going to find it very difficult to cope with these people,” said Al Jazeera’s Diplomatic Editor Jaes Bays, reporting from the UN headquarters in New York.
“They don’t have the food or resources to look after them.”
The US embassy said on its Twitter account late on Tuesday that that all of its citizens in the country should “depart immediately”. The account tweeted that it would outline evacuation options on Wednesday morning.
UN troops in the country have the mandate to use deadly force if necessary to protect civilians, Security Council President Gerard Araud told Al Jazeera.
“Fighting is on ethnic lines, which could result in a very dangerous situation,” said Araud, the French ambassador to the UN.
Poor communications in Juba, where the mobile phone system has not operated since Monday 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.
Kiir said on Monday the fighting between army factions was a bid to seize power by the former vice president, Riek Machar, whom he sacked in July.
The two men, from different ethnic groups, which have clashed in the past, have long been political rivals. Analysts said divisions between them run deep and rivalries in army ranks have long simmmered.
At least 10 senior former government officials have been arrested, including six cabinet ministers, said Information Minister Michael Makuei Lueth. The government named the men on its website.
Residents near Juba airport, which has been closed since Monday, were woken before dawn on Tuesday by gunshots and blasts, a UN worker said. Others also reported bouts of shooting.
The streets of Juba were deserted, with only military vehicles to be seen and civilians barricaded in their homes.
Kiir had said in a statement on Monday that security forces had regained control, although a curfew had been imposed.
“The attackers went and [the] armed forces are pursuing them,” Kiir said. “I promise you today that justice will prevail.”
“We will of course do everything we can do protect people. Many people who are coming require health care of all types,” Toby Lanzer, UN deputy special representative for South Sudan, told Al Jazeera .
“Some people have been injured. We’ve got challenges of a variety – and the water and sanitation situation is also something that we are grappling with.”
Tension had been mounting in South Sudan since Kiir’s sacking of Machar. The men belong to different ethnic groups – Kiir to the Dinka, the most powerful, and Machar to the Nuer, but it is not clear whether this latest tension is due to ethnic or political divisions.
Machar, who has expressed a willingness to contest the presidency in 2015, told Al Jazeera in July that if the country is to be united it cannot tolerate “one man’s rule or it cannot tolerate dictatorship”.
His sacking, part of a wider dismissal of the entire cabinet by Kiir, had followed reports of a power struggle within the ruling party.
South Sudan’s government has struggled to create a functioning state since it declared independence from Sudan in 2011, after years conflict with Khartoum during a war that often saw south-south clashes.