WASHINGTON — South Sudan is in many ways an American creation, carved out of war-torn Sudan in a referendum largely orchestrated by the United States, its fragile institutions nurtured with billions of dollars in American aid. But a murky, vicious conflict there has left the Obama administration scrambling to prevent the unraveling of a major American achievement in Africa.

With at least 1,000 people killed in fighting between government and rebel forces, and with disturbing reports of ethnically motivated atrocities by both sides, President Obama faces the real prospect that South Sudan could become Africa’s next failed state.

On the first morning of his Hawaii visit, two weeks ago, Mr. Obama woke up to an urgent conference call with his national security team about the fighting in South Sudan, and efforts to evacuate American citizens. He has been briefed on it every day since, his aides said — a level of attention unheard-of for any other crisis in that part of Africa.

As with Syria and other sectarian conflicts, Mr. Obama does not have many good options. With no plans for American military intervention, the United States is frantically brokering peace talks between the warring factions while trying to fortify a United Nations peacekeeping force. It is also consulting Uganda and Ethiopia, whose troops could intervene to prevent rebels from seizing South Sudan’s capital, Juba.

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“None of us is naïve; this is a real and profound crisis,” said Gayle Smith, the senior director for global development and humanitarian issues at the National Security Council, who is helping direct the response. “But we’ve got a long history, and we’ve got some leverage.”

On Friday, after days of pressure by an American special envoy, the two sides began talking, through a mediator, in the Ethiopian capital, Addis Ababa. The White House has threatened to cut off aid to anyone who seizes power, and it is no longer providing training for South Sudan’s military, the Sudan People’s Liberation Army.

Still, the fighting rages on, prompting the State Department to withdraw more personnel from its embassy in Juba. It has already evacuated hundreds of Americans and ringed the embassy with 45 American soldiers to protect it from an attack like that on the diplomatic compound in Benghazi, Libya, in September 2012.

Unlike most African countries, South Sudan has a powerful constituency in Washington, not only in the White House but also on Capitol Hill, where lawmakers have championed its Christian population against persecution by the Muslim north. The administration of George W. Bush played a central role in negotiating an end to Sudan’s protracted civil war, setting the stage for the 2011 referendum that split the south from the north.

For this administration, too, South Sudan carries special resonance. Mr. Obama’s national security adviser, Susan E. Rice, is an Africa expert, who in 2006 called for the United States to intervene militarily to prevent the slaughter of civilians in Darfur. Aides say Ms. Rice has briefed the president by phone almost every day during his vacation, and before Christmas, she recorded a message to the people of South Sudan, warning that “those who have committed acts of violence against civilians must be held accountable.”

The American ambassador to the United Nations, Samantha Power, made her name by arguing for intervention in countries to avert genocide and recently returned from a visit to another strife-torn country, the Central African Republic. At the United Nations, she drafted a resolution to increase the number of peacekeepers in South Sudan.

Video

A Desperate River Crossing

Residents of Bor, a city in the Republic of South Sudan, fled deadly violence there by taking ferries across the White Nile to Awerial, where an estimated 76,000 displaced people are stranded.

By Nicholas Kulish and Erica Berenstein on Publish Date January 3, 2014. . Watch in Times Video »

Secretary of State John Kerry witnessed the referendum while a senator — and has reminded South Sudan’s president, Salva Kiir, of that in repeated phone calls urging him to reconcile with his former vice president, Riek Machar. Their political feud revived barely dormant ethnic tensions within the country.

The United States, a senior administration official said, is getting “a lot of very disturbing reports about targeted killings of Nuer, as well as targeted killings of Dinka” — the two main ethnic groups in South Sudan. The specter of mass atrocities has rattled the administration, which on Friday pledged an additional $49.8 million in humanitarian aid for the roughly 180,000 people driven from their homes by the fighting.

“We can’t allow the carnage to go on; we can’t allow the capital to be overrun,” said Tom McDonald, who worked on Sudan issues as the American ambassador to Zimbabwe during the administration of Bill Clinton. “We have too much to lose; we’ve put too much into this.”

Mr. McDonald, now a lawyer at Baker Hostetler, said the administration should pursue a dual track, encouraging reconciliation while developing plans to help Uganda and Ethiopia with military intervention in the event that diplomacy fails. Uganda’s president, Yoweri Museveni, has threatened to intervene if the rebels do not agree to a cease-fire.

While the United States is highly unlikely to commit its own troops, Mr. McDonald said, it could provide planes to transport Ugandan soldiers or share intelligence on rebel positions with Ethiopia’s air force. American officials said that they hoped that Uganda’s warning would be enough of a deterrent and that intervention would not be needed.

In the meantime, said Grant T. Harris, the senior director for African affairs at the National Security Council, the United States is pushing to expand the size and mission of the United Nations’ peacekeeping force, which currently numbers more than 7,600 and is struggling to protect an estimated 45,000 refugees who have swarmed its compounds.

For now, American diplomacy is being handled by a special envoy, Donald E. Booth, an experienced Africa hand who has been ambassador to Ethiopia, Liberia and Zambia. But some experts say higher-level officials, like Ms. Rice, will eventually have to get involved.

“The last thing I worry about is these guys not knowing about, or not understanding, what’s going on there,” said John Prendergast of the Enough Project, a nonprofit, anti-genocide organization.

The problem, analysts say, is that the United States does not have the influence it had before 2011. Then, the South Sudanese needed American aid and support for a referendum. Now they have independence and more than $1 billion a year in oil revenue that used to go to the north.

“Very quickly after independence, we saw increasingly authoritarian instincts, not just on the part of Salva Kiir, but all the members of the South Sudanese political elite,” said Cameron Hudson, a former State Department official who is now the policy director at the United States Holocaust Memorial Museum.

This time around, powerful neighbors like Ethiopia, Uganda and Kenya are taking a lead role in trying to broker peace.

Still, said Sara Pantuliano, head of the Humanitarian Policy Group at the Overseas Development Institute in London, “I do think that the U.S. is probably the only country that can push the two sides to sit down and have serious talks. But they really need to want it at a very high level.”

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