Shortly after Haley left the camp, UN security guards fired tear gas to disperse the crowd of more than 100 residents who looted and destroyed the office of a charity operating there, an aid worker at the camp said.
The aid worker spoke on condition of anonymity out of safety fears.
Haley, in the middle of a three-country African visit, met earlier today with Kiir over the country's long civil war.
The United Nations confirmed the incident with Haley, saying camp residents "became upset that she was not able to meet with them, due to time constraint." The US Embassy did not comment on Haley's evacuation.
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Frustration has been growing inside and outside South Sudan over the conflict that has killed tens of thousands and created Africa's largest displacement of civilians since the Rwanda genocide in 1994.
The UN said a "petition" was delivered before Haley's departure.
"We are disappointed by what we are seeing. This is not what we thought we were investing in," Haley said in remarks later released by the UN. "What we thought we were investing in was a free, fair society where people could be safe and South Sudan is the opposite of that."
In his meeting with Haley, South Sudan's president appealed for the Trump administration to stay engaged with his devastated country. According to a statement by his office, Kiir "emphasised his commitment" to end the conflict through peace talks that took place in the capital, Juba, last week and are expected to resume in December.
"All disputes can only be resolved through dialogue and not arms," Kiir told Haley, the statement said. Multiple attempts at peace deals have failed in the past.
South Sudan plunged into civil war in late 2013, and the country faces mass displacement, starvation and allegations of government corruption and war crimes. More than 2 million people have fled the country.
Before her visit to the UN camp, Haley said on Twitter that she hopes South Sudan's peace process succeeds. "The pain in the stories of refugees from S Sudan is a reminder we can't look away. We can't let armed conflict be their only choice," she said.
Rights groups have urged the United States to take a tougher approach to Kiir's government.