Obama said South Sudan's leaders have a responsibility to help protect Americans, who came under fire hours earlier during an evacuation attempt.
While vacationing in Hawaii, Obama spoke by telephone with national security aides, the White House said. He told his team to work with the U.N. to keep evacuating Americans from Bor, where some of South Sudan's worst violence over the last week has played out.
Among those briefing the president was his national security adviser, Susan Rice, who a day earlier recorded an audio message to South Sudan's leaders urging them not to allow the nation "to be torn apart by violence and suffering."
"This conflict can only be resolved peacefully through negotiations," the White House said in a statement Saturday. "Any effort to seize power through the use of military force will result in the end of longstanding support from the United States and the international community."
Secretary of State John Kerry called President Salva Kiir to urge the South Sudanese leader to avoid ethnic conflict, preserve the welfare of those fleeing the conflict and protect U.S. citizens there. Kerry was sending a special envoy to the region and told Kiir that South Sudan's challenges require leadership and political dialogue, the State Department said.
The U.S. has been working to evacuate American citizens and nonemergency government personnel from the African country, and last week shut down most embassy operations in the capital of Juba after what South Sudan's president described as an attempted coup.
On Saturday, gunfire hit three U.S. military aircraft trying to evacuate Americans in a remote region that has become a battle ground between the country's military and renegade troops, officials said. The three CV-22 Ospreys were about to land in Bor when they were hit and subsequently diverted to Entebbe, Uganda.
Four U.S. troops wounded in that incident are in stable condition, the White House said.
The violence has killed hundreds and has world leaders worried that a full-blown civil war could ignite in South Sudan. The South fought a decades-long war with Sudan before a 2005 peace deal resulted in a 2011 referendum that saw South Sudan break away from the North, taking most of the region's oil wealth with it.
In the call with U.S. officials, Obama directed his team to keep him abreast of developments in South Sudan. Even when on vacation, the president travels with senior-level national security aides who keep in close contact with Washington and brief him regularly on issues of concern.
"The president underscored the urgency of helping to support efforts to resolve the differences within South Sudan through dialogue," the White House said. "South Sudan's leaders must know that continued violence will endanger the people of South Sudan and the hard-earned progress of independence."