The medial charity Medecin Sans Frontiers (MSF) said on Sunday that it is "extremely worried" after losing contact with 130 staff in the town of Pibor.
The MSF compound and hospital was taken and torched by Lou Nuer attackers on Saturday. MSF spokesman, Parthesarathy Rajendran, told news agencies that they had only been able to get in touch with 13 members of staff, and believe the rest fled into the bush to escape the attack.
He urged both sides in the conflict to respect MSF facilities because the charity was the only health-care provider in the area.
Almost all residents of Pibor have fled in recent days, amid fears of an impending assault as about 6000 Lou Nuer moved toward Pibor following a large scale attack on the town of Likuangole to the north.
The South Sudan People's Liberation Army has a battalion of soldiers protecting Pibor. The United Nations Mission in South Sudan deployed more peacekeepers there this week to assist the government in protecting any civilians that remained.
In a statement issued Sunday, President Salva Kiir said he had ordered more than 3000 additional troops and 800 police offiers into Jonglei to increase efforts to stop the violence and protect civilians.