Thousands are believed to have been killed in more than a week of violence, with reports of bodies piled in mass graves amid escalating battles between troops loyal to President Salva Kiir and those backing his rival Riek Machar, a former vice president who was sacked in July.
Government forces celebrated late Tuesday the recapture of Bor from forces loyal to Machar after the army stormed the strategic town, but battles raged elsewhere including Malakal, capital of oil-producing Upper Nile state.
Information Minister Michael Makwei denied rebel claims they had seized it.
"There is fighting now in Malakal since morning between the government forces and the rebels," Makwei told AFP. "It is not true that the rebels have taken over."
An AFP correspondent who visited Bor Wednesday said that bodies littered the streets and stores were looted, with occasional gun shots still ringing out even as civilians poured back into the town to return home.
Fighting has spread to half the country's 10 states, the United Nations said, with hundreds of thousands fleeing to the countryside and others flooding UN bases seeking shelter.
The UN humanitarian chief in the country, Toby Lanzer, said Tuesday there was "absolutely no doubt in my mind that we're into the thousands" of dead, the first clear indication of the scale of the conflict engulfing the world's youngest country.
Earlier, UN rights chief Navi Pillay said a mass grave had been found in the rebel-held town of Bentiu and cited reports of at least two more in Juba.
Around 15 bodies were found in one site in Bentiu, with another 20 bodies at a nearby river.
In Juba, the UN mission was more cautious, confirming the 15 killed but saying it was still "investigations reports of such atrocities".
The official toll nationwide has stood at 500 dead for days, but aid workers have said the number killed was likely far higher.
Pope Francis called Wednesday for "social harmony" and warned the violence was "threatening peaceful coexistence".
'Chaos' could engulf young country
Witnesses recount a wave of atrocities, including an orchestrated campaign of mass killings and rape.
"There are now people who are targeting others because of their tribal affiliation," Kiir said in a Christmas message to the country, where the population is roughly divided between Christians, Muslims and traditional beliefs. "It will only lead to one thing and that is to turn this new nation into chaos."
Government forces have also said they are preparing to take back the town of Bentiu, capital of South Sudan's most important oil region Unity state, now in the hands of a powerful army commander who mutinied last week to join Machar.
Oil production, which accounts for more than 95 percent of South Sudan's fledgling economy, has been dented by the violence, with oil workers evacuated.
Bor's recapture, without major resistance by the rebels, lifted a nearly week-long seige of the town, where some 17,000 civilians fled into the overstretched UN compounds for protection, severely stretching limited food and supplies.
"Most of the rebels who were in the town are on the run," Makwei said.
UN peacekeepers had spent days bolstering fortifications ahead of the army assault, after militia gunmen last week stormed a UN compound in the Jonglei outpost of Akobo, killing two Indian soldiers and about 20 ethnic Dinka civilians sheltering there.
UN force boosted by 6,000
The unrest has taken on an ethnic dimension, pitting Kiir's Dinka tribe against Machar's Nuer.
Machar said he was ready to accept Kiir's offer of talks, following days of shuttle diplomacy by African nations and calls from Western powers for an end to the fighting.
"We want democratic, free and fair elections. We want Salva Kiir to call it a day," Machar said, listing his demands Tuesday.
US Secretary of State John Kerry called both men and urged them to "accept a cessation of hostilities and begin mediated political talks", the State Department said.
Late on Tuesday, the UN Security Council voted to send nearly 6,000 extra soldiers and police to South Sudan, nearly doubling the UNMISS force to 12,500 troops and 1,323 civilian police.
But UN chief Ban Ki-moon, who requested the reinforcements, warned the force "will not be able to protect every civilian in need in South Sudan".
The US military deployed a "platoon-sized" Marine contingent to neighbouring Uganda, while nearly 100 US troops are already on the ground in South Sudan. Four were wounded on Saturday when their aircraft was shot at during an evacuation operation.
South Sudan gained independence in July 2011 to become the youngest country in the world, born out of a bloody decades-long struggle for independence from Sudan. It remains a fragile state with deep ethnic divisions.
Kiir has accused Machar of starting the fighting by attempting a coup, while Machar says the president has exploited tensions within the army to carry out a purge.
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