The U.S. Africa Command says four U.S. service members were wounded as a result of gunfire directed at their military aircraft.
The incident took place on Saturday as U.S. forces were trying to rescue Americans from Bor, a town north of the capital, Juba. The mission was aborted and all three planes were diverted to neighboring Uganda.
U.S. President Barack Obama on Thursday sent 45 U.S. service personnel to the region on a mission he said is aimed at protecting U.S. personnel and the U.S. Embassy.
In a White House statement issued Saturday, Obama stressed the importance of the U.S. evacuation mission and said South Sudan's leaders have a responsibility to assist the U.S. efforts.
South Sudan's government says rebels have overrun Bor, which has been the scene of some of the country's worst fighting over the past week.
The violence erupted after President Salva Kiir, a Dinka, accused former vice president Riek Machar, a Nuer, of attempting a coup. The Juba government says more than 500 people have been killed, and the unrest has forced tens of thousands of people to flee from their homes.
Evening and overnight curfews have been enforced in the capital, where military tanks and armored vehicles remain on the streets and the airport has been overrun with people attempting to flee situation.
"Hundreds of people [are] trying to leave by charter flight or by any means possible, even with a single bag, because they are so worried that this violence has just spiraled out of control already and they don't trust that the government of South Sudan can protect them any longer," said Juba-based VOA correspondent Hannah McNeish, explaining that many fear what started as a political power struggle is turning into a deeply ethnic conflict.
The prevailing unrest within the capital, she added, is nothing compared to events unfolding in other parts of the country.
"We've got fighting in Jonglei state, where rebels have taken over the state capital, Bor," she said. "We've also got heavy fighting, apparently, in Unity state, where the oil fields and rebels are battling government forces for control of these."
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U.S. Secretary of State John Kerry says he is sending a special envoy to South Sudan to encourage talks between opposing factions. Ambassador Donald Booth is heading to the region as soon as possible.
The U.N. Security Council president Gerard Araud said Friday that South Sudan's President Kiir and former vice president Machar have agreed to "unconditional dialogue" despite their recent history of bitter recriminations. Mediators from East African countries met with Kiir Friday in what they called productive talks, but what form the Kiir-Machar "dialogue" will take is unclear.
On Friday, the U.N. said at least 11 civilians and two peacekeepers had been killed in an attack a day earlier on a U.N. base in the town of Akobo.
The U.N. Mission in South Sudan says the peacekeepers and civilians were shot after about 2,000 armed youth, believed to be ethnic Nuers, surrounded the base and opened fire on members of the Dinka ethnic group taking shelter at the U.N. compound.
About 35,000 civilians are believed to have fled to U.N. compounds since the latest unrest began.
South Sudan is the world's newest country, gaining its independence from Sudan in 2011.
Some information was provided by Reuters, AP and AFP.