The South Sudan Media Authority (SSMA) has ordered the closure of the United Nations-owned Radio Miraya citing failure to comply with broadcasting regulations.
The media regulator claimed the station failed to acquire a new operating licence despite having been notified four times between June 2017 and February 2018.
"The management of Radio Miraya has not responded which is a clear violation and non-cooperation with the media authority's orders," a circular issued by SSMA on Friday reads.
The directive ordered the radio to stop broadcasting with immediate effect.
But the UN Mission in South Sudan (UNMISS) chief of Radio Miraya, Ratomir Petrovic, said the station will stay on-air pending talks with government.
"UNMISS is in discussion with the government while Radio Miraya continues to broadcast across the country," he said.
Radio Miraya operates under UNMISS and according to international treaties.
Its operations are protected by the Status of Forces Agreement (SOFA) signed by the UN and the South Sudanese government.
Last year, the media regulator ordered fresh registration of all media houses and journalists, and threatened unspecified consequences in case of defiance.
The media sector remains the most threatened in the country since civil war broke out in December 2013.
Many journalists complain of harassment, detention and some have lost their lives in the line of duty.