Civil war broke out in South Sudan in December 2013 when President Salva Kiir accused his former deputy Riek Machar of plotting a coup. The fighting has split the country along ethnic lines and driven it to the brink of collapse.
A peace deal signed between the government and rebels almost a year ago has so far failed to end the conflict. And last month Juba was rocked by several days of heavy fighting between Kiir's forces and those loyal to Machar.
Secretary General Ban Ki-moon said late Tuesday he was "concerned about allegations that UNMISS did not respond appropriately to prevent this and other grave cases of sexual violence committed in Juba."
He was referring to the UN peacekeeping mission in South Sudan, called UNMISS.
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Ban said that in the July 11 incident one person was killed and several civilians were raped and beaten by men in uniform.
The UN leader said he had launched "an independent special investigation to determine the circumstances surrounding these incidents and to evaluate the Mission's overall response."
He also called on the government to probe these acts of violence and prosecute those involved.
The US ambassador to the United Nations, Samantha Power, reported assaults and rapes of civilians, including humanitarian aid workers and journalists, by South Sudanese soldiers at the hotel.
"South Sudan's leaders must investigate this incident and hold accountable the individuals responsible for these cowardly and brutal assaults," Power said in a statement.
At the request of the US, she said, the government sent a response force to the hotel compound.
UN troops in South Sudan have come under heavy criticism after last month's fighting, for failing to protect civilians including women and girls raped near a UN base in Juba.
The UN says it has documented at least 200 cases of rape in July alone by men in uniform, mainly troops loyal to president Kiir.