The U.N. Mission in South Sudan said it relocated a staff member to neighboring Uganda until authorities can reach a decision on her future status.
Barnaba Marial Benjamin, a spokesman for the South Sudanese government, was quoted by the BBC as saying the order was given because the UNMISS officer was "reporting on human rights issues that she could not verify and has been publishing without justifications."
Hilde Johnson, U.N. special envoy for South Sudan, said the order was a breach of South Sudan's legal obligations under the U.N. Charter.
"Human rights monitoring, investigation and reporting, and building capacity, is a core element of the mandate of UNMISS which must be protected," she said in a statement.
Johnson added she raised the issue with South Sudan's President Salva Kiir. Human rights violations, she added, were part of the region's core struggles during the Sudanese civil war.
South Sudan gained independence last year as part of a 2005 peace that ended a civil war that lasted more than 20 years.