The US State Department said Wednesday that it was "aware of the incident."
South Sudan's foreign ministry said it has recalled a US-based diplomat after "an alleged rape incident" in New York City, suspending the official until an ongoing investigation is completed.
"It is with regret that our diplomat was involved in an alleged rape incident with... (a) New York City resident," the ministry said in a statement published on the government's official Twitter page late Thursday.
"The diplomat in question is now back in South Sudan and has been suspended from his duties, awaiting the outcome of this investigation," the statement said.
"Sexual misconduct in any shape or form is heinous and wholly unacceptable," it said, adding that "a specialised committee" was examining the case.
The statement did not elaborate on the allegations, but US media reports said the diplomat was accused of forcibly entering the victim's Manhattan apartment and raping her on Sunday.
Police initially took him into custody before releasing him hours later after he invoked diplomatic immunity.
The US State Department said Wednesday that it was "aware of the incident... involving a diplomat accredited to the UN."
"We take these allegations very seriously and are working closely with the New York Police Department and the Mayor's Office of International Affairs," State Department spokesman Vedant Patel said, without offering further details.
In March, the UN accused members of South Sudan's government of committing human rights violations "amounting to war crimes" in the country's southwest, urging investigations against dozens of individuals, including for sexual violence and abuses against children.
The world's newest nation has suffered from chronic instability since independence in 2011, with the UN repeatedly criticising South Sudan's leadership for its role in stoking violence, cracking down on political freedoms and plundering public coffers.
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