Medecins Sans Frontieres (MSF) said on Tuesday that it had suspended activities in the northeast of South Sudan.
The announcement came a day after unidentified armed men stormed one of its compounds, looted property and burned equipment.
MSF said in a statement that none of its staff members was injured during the incident on Monday in Maban in Upper Nile State.
"A group of unidentified armed men broke into the MSF office and compound in the morning, looting the organisation and staff’s property, burning down a tent full of equipment, and destroying most of the vehicles and communication devices.
"The attack has forced MSF to suspend the majority of its medical support to the host communities and the refugee population in the Maban area," the statement said.
South Sudan has been mired in civil war since 2013 after President Salva Kiir fell out with his then-vice president Riek Machar. Fighting has often been along ethnic lines and has killed tens of thousands of people, devastated the oil-based economy and displaced at least 4 million people.
MSF said its suspension of activities would leave some 88,000 people with limited access to aid.
Also on Monday, the UN refugee agency UNHCR said its facilities in the same area were invaded and said the attackers had complained that aid groups had overlooked local residents when hiring staff.
UNHCR said 10 other organisations - including MSF - and the offices of the Commission for Refugee Affairs (CRA) had been attacked and looted. It said Upper Nile's Maban County hosts over 144,000 people in four refugee camps.
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