South Sudanese President Salva Kiir has declared a state of emergency in two states, according to the government’s official Twitter account.

The decree issued on Wednesday covers Unity and Jonglei, where government troops and rebel forces loyal to former vice president Riek Machar have been engaged in fighting.

The declaration came as the rival factions were set to open talks in Ethiopia on Thursday, aimed at bringing an end to the nearly three-week-old conflict, despite reports of an imminent military showdown in Jonglei.

Sources said government and rebel negotiators arrived in the Ethiopian capital Addis Ababa on Wednesday.

Ethiopian government spokesman Getachew Reda said the talks would focus on “monitoring mechanisms for the ceasefire”.

Following the fall of Bor, Jonglei’s state capital, into the hands of the rebels on Tuesday, the government and rebels loyal to Machar agreed to meet for talks.

The South Sudan government, however, refused to call it a ceasefire, saying negotiators must first agree on “mechanisms” for talks to move forward.

Fierce battle imminent

For his part, Kiir named eight negotiators to represent his government in the proposed talks in Ethiopia, Al Jazeera’s Mohammed Adow reported from the South Sudanese capital Juba on Wednesday.

Despite the preparations for the talks, thousands of government troops were making their way to Bor in an effort to wrest back control of the Jonglei state capital, setting up another possible fierce battle with rebels.

Our correspondent quoted government sources as saying that “it is just a matter of time” before they retake Bor, which was captured by rebels on Tuesday.

Fighting is also going on in other fronts like Mayom and Malakal, he said.

Violence first erupted in South Sudan on Dec. 15, when Kiir accused Machar of attempting a coup.

Machar has denied this, in turn accusing Kiir of conducting a violent purge of his opponents.

The fighting has since spread across the country, with the rebels seizing several areas in the oil-rich north.

Thousands of people are feared dead, U.N. officials said, while close to 200,000 civilians have been forced to flee their homes – many seeking refuge with badly overstretched U.N. peacekeepers.

Jacob Kurtzer, a representative of the International Committee of the Red Cross, told Al Jazeera that refugees need immediate help.

The U.N. has said it will do everything it can to prevent further “terrible acts of violence” in South Sudan.

“We have seen terrible acts of violence in the past two weeks, there has been killings and brutality, grave human rights violations and atrocities committed,” Hilde Johnson, U.N. special representative to South Sudan, told Al Jazeera.

The conflict has been marked by an apparent surge in ethnic violence pitting members of Kiir’s Dinka tribe against Machar’s Nuer community.

Continuing ‘atrocities’

The U.N. Mission in South Sudan (UNMISS) said “atrocities are continuing to occur” across the country despite efforts to negotiate a ceasefire.

“UNMISS is gravely concerned about mounting evidence of gross violations of international human rights law that have occurred in South Sudan during the past 15 days,” it said in a statement, reporting “extra-judicial killings of civilians and captured soldiers” and the “discovery of large numbers of bodies” in Juba, Bor and Malakal, the main town in oil-producing Upper Nile state.

UNMISS has said it is “actively collecting information” on the atrocities to be used for future official investigations.

U.N. Secretary-General Ban Ki-moon has already given warning that senior South Sudanese figures “will be held personally accountable” for any crimes against humanity.

Johnson, the U.N. special representative, has said there is evidence that South Sudanese citizens are being targeted “on ethnic grounds”.

“This can lead to a perpetual cycle of violence that can destroy the fabric of the new nation,” she said.

“We need to do everything possible to prevent such a cycle of violence between communities of South Sudan.”

However South Sudan political analyst Matthew LeRiche told Al Jazeera the fighting is “very much a political struggle” rather than an ethnic conflict.

He noted that Kiir and Machar belonged to the same government and the same party, until they split due to political differences.

Published under an agreement with Al Jazeera.

WFP has launched an operation including the use of helicopters to bring urgently-needed food assistance to tens of thousands of people who have fled to hard-to-reach areas to escape violence in Pibor County, Jonglei State. Credit: UN Photo/Martine Perret

By Roger Hamilton-Martin
UNITED NATIONS, Jul 26 2013 (IPS)

Following fighting in the South Sudan state of Jonglei , the United Nations is trying to coordinate a humanitarian effort to help tens of thousands of people who have fled to the bush. The World Food Programme (WFP) has launched an operation to provide food for those who have escaped the conflict.

“We believe these people need food now and cannot wait for much longer after hiding in the bush for weeks,” said Chris Nikoi, WFP South Sudan country director, in a statement on Tuesday.

The agency is requesting 20 million dollars to fund emergency assistance for 60,000 people through December.

“The Lou Nuer have a longstanding grudge against the Murle, which of course is a two-way street,” Sudan expert Eric Reeves told IPS. “But over the past years these tensions have come to a boil and mutual retaliations are extremely violent.” Retaliation is often in response to cattle looting by neighbouring communities, he said.

It has proven difficult for humanitarian groups to gain access to the large number of people who have been affected by the conflict in the state, South Sudan’s largest, in part because of the fighting and in part due to the lack of passable roads.

The international medical humanitarian organisation Médecins Sans Frontières says it has “treated scores of people and is attempting to reach thousands more who are hiding in the bush… [an] MSF emergency team is attempting to reach tens of thousands of people hiding in unsafe, malaria-infested swamps, without access to safe drinking water, food, or medical care.”

John Tzanos, who heads the MSF team in Pibor County, said in a statement, “They [civilians] are afraid to seek medical care in towns so it is essential for us to intervene where they are so that all those in need can access treatment.” With the latest wave of violence over, there is still no word on the number of casualties.

“We don’t have any figures [on fatalities] at all,” the acting humanitarian coordinator of the U.N. Office for the Coordination of Humanitarian Affairs (OCHA) in Jonglei, Dr. Yasmin Haque, told IPS.

“The challenge has been access, and now we have been able to secure additional funding which has improved our air transport capacity. We have also had a strengthening and better communication in getting security clearances and information in getting our flights to those areas.

“The biggest need is going to be food, and getting the amounts required into the areas is going to be many trips over many days,” she said. Haque said U.N. agencies were working with the government, especially the Relief and Rehabilitation Commission, and were also coordinating aircraft with the army, the SPLA.

“People have been afraid to return to the more populated areas where they have been [living],” she said. “Fear of insecurity and fighting is keeping people away from the main county locations.”

Another spokesperson for OCHA told IPS, “We have already begun to register the people displaced, and have begun to distribute household items and emergency shelter to people who have been living in the bush, exposed to the elements.”

OCHA has appealed for more resources from the international community, and noted that during the rainy season, which lasts from May to October, up to 90 percent of roads in Jonglei state are inaccessible, so aid must be delivered by air.

There are also allegations that the Sudanese government in Khartoum has been exacerbating the conflict by supplying rebel Murle leader David Yauyau with weapons.

The difficulty in tracking Yauyau’s rebels has made it hard for U.N. agencies to keep the peace and supply civilians with necessary aid. Yauyau’s current rebellion has been running since April 2012, for what he claims to be the rights of the Murle.

In an interview last year, Yauyau said, “This time around, we are fighting for the people of South Sudan, the minority communities like the Murle and the others…They don’t have a voice… they don’t have rights to live on the land. We don’t have a voice in the government. We are struggling together with them and we’ve lost some of our sons.”

There are also allegations of human rights abuses perpetrated by the government.

In an open letter to the government written in June, Reeves and three other signatories said that “over the past several years – but the last six months in particular – South Sudan government security forces have engaged in a campaign of violence against civilians simply because they belonged to a different ethnic group or they were viewed as opponents of the current government.”

The U.N. has also condemned the government for what it calls “serious human rights violations” allegedly committed by elements within the South Sudanese Army in Pibor County.