On Thursday, armed youths breached a UN compound in Jonglei state, causing an unknown number of casualties.
"Unfortunately, just this very morning such militia groups have targeted and killed three soldiers from India in South Sudan," India's UN Ambassador Asoke Mukerji told a UN meeting on peacekeeping Thursday evening.
It was the first announcement of UN personnel killed in this week's upsurge of violence. Pakistan's UN Ambassador Masood Khan asked for a minute of silence, and diplomats rose to pay tribute to the fallen soldiers.
In the capital, Juba, emergency evacuation flights took away American and British citizens, aid workers and United Nations personnel to escape the violence.
An internally displaced man holds his son inside a United Nations Missions in Sudan compound in Juba. (Reuters Photo)
UN Secretary-General Ban Ki-moon again urged political dialogue.
"The future of this young nation requires its current leadership to do everything possible to prevent South Sudan descending into the chaos that would be such a betrayal of the ideals behind its long struggle for independence," a statement from his office said late Thursday.
South Sudan's government declared that its security forces "are in absolute control of the situation," but admitted later Thursday that the central government had lost control of Bor, the capital of the country's largest and most populous state, where barrages of gunfire were reported.
"The situation in South Sudan can be best described as tense and fragile. If it is not contained, it could lead to ethnic cleansing," said Choul Laam, a top official with the ruling Sudan People's Liberation Movement, who spoke in Nairobi, Kenya.
Violence broke out late Sunday when the presidential guard splintered along ethnic lines. Guards from the president's majority Dinka tribe tried to disarm guards from the Nuer ethnic group, said Laam. Violence in Juba spiraled from there, and then extended out into the country.
"The awful accounts of killings in Juba may only be the tip of the iceberg," said Daniel Bekele of Human Rights Watch. "Government officials - whatever their politics - need to take urgent steps to prevent further abuses against civilians and quickly deescalate rising ethnic tensions."
President Salva Kiir earlier said an attempted coup had triggered the violence, and the blame was placed on ousted Vice President Riek Machar, an ethnic Nuer.
A young boy, injured while fleeing from clashes, rests at a medical clinic inside the United Nations compound on the outskirts of Juba. (Reuters Photo)
Machar disputed Kiir's allegations that he had attempted a coup, but said he wants Kiir out of power.
"We want him to leave. We want him to leave. That's it," Machar told Radio France Internationale. "He can't unite the people and he kills them like flies."
Machar, an influential politician who is a hero of the brutal war of independence against Sudan, is Kiir's rival for top leadership of the Sudan People's Liberation Movement party. Tensions had been mounting since Kiir fired Machar as his deputy in July. Machar later said he would contest the presidency in 2015.
Regardless of the cause, the South Sudan government said the violence has already killed up to 500 people.
Armed ethnic Nuer youths breached a UN compound in the tiny Jonglei village of Akobo, near the Ethiopian border, to reach civilians believed to be Dinkas seeking shelter there, said UN spokesman Farhan Haq in New York. "We fear there may have been some fatalities but can't confirm who and how many at this stage," Haq said.
At the time, 43 Indian peacekeepers, six UN police advisers and two UN civilian employees were present at the base, as were about 30 South Sudanese who had sought shelter, according to the UN mission in South Sudan. The mission said it would dispatch aircraft early Friday to evacuate UN personnel who remain at the base.
South Sudan's capital was mostly peaceful Thursday, and the government tried to assure the UN and foreign embassies "that civil tranquility has been fully restored."
US President Barack Obama said in a letter to Congress that 45 military personnel were dispatched to South Sudan on Wednesday to protect US citizens and property.
Countries such as the US, Britain, Italy and Germany continued to evacuate residents. A plane with a mechanical malfunction blocked the runway during the day, jamming up inbound and outbound flights.
The US evacuation plane - the fourth group of Americans flown out in two days - was eventually able to take off heading for Kenya. "Runway clear. Wheels up," the embassy said on Twitter. Two military flights and a charter took off on Wednesday. Britain's evacuation plane landed in Uganda late Thursday.
The government said it lost control of Bor, the capital of Jonglei state, to forces loyal to Machar. Gunfire was reported early and late in the day, and the UN used four helicopters to transport 75 people - a mix of aid workers and UN staff - to Juba, said Challiss McDonough, a spokeswoman for the UN's World Food Program.
"We lost control of Bor to the rebellion," said Philip Aguer, the South Sudanese military spokesman.
Aguer said renegade officers wrested control of the town from loyalist forces. At least 19 civilians had been killed in Bor, said Martin Nesirky, a spokesman for the UN secretary-general's office, citing figures from the South Sudan Red Cross.
In oil-rich Unity state, fighting broke out in oil fields on Wednesday and Thursday, said Mabek Lang De Mading, the state's deputy governor. He said five people died Wednesday and 11 on Thursday.
Foreign ministers from neighboring countries Kenya, Ethiopia, Uganda and Djibouti traveled to South Sudan to try and diffuse the crisis.
Human Rights Watch said Thursday that South Sudanese soldiers fired indiscriminately in highly populated areas of Juba earlier in the week and targeted people for their ethnicity.
Civilians fleeing violence seek refuge at the UNMISS compound in Bor, South Sudan. (AP Photo)
Citing witnesses and victims, the group reported that "soldiers specifically targeted people from the Nuer ethnic group." In some cases, the group added, the Dinka may have been targeted by Nuer soldiers.
An estimated 20,000 people have sought refuge at two UN compounds in Juba and another 14,000 in Bor. UN officials warned of a humanitarian crisis.
Deputy secretary-general Jan Eliasson said in New York on Thursday that the UN will do its best to protect those who have sought refuge. "Clearly, civilians are in danger," said Eliasson.