Mundri Relief & Development Association (MRDA), a long-term Christian Aid partner has been attacked in recent weeks.
The conflict in South Sudan started nearly two years ago after a political struggle between the President and former Vice President.
It quickly escalated along ethnic lines and rapidly spread across the country.
Since then it is thought that tens of thousands of people have been killed, more than 1.6 million have been internally displaced and around 600,000 refugees have fled the country to escape the ongoing violence.
Rosie Crowther, Christian Aid Emergency Programme Officer, who is based in the capital, Juba, said: "If we manage to raise humanitarian funds to help the people affected by this latest onset of fighting, then as soon as access becomes possible MRDA's strong roots in the area will mean it is well-placed to respond quickly.
"Access is difficult in some areas of South Sudan so it's essential to respond to urgent humanitarian needs as soon as there is a break in fighting."
Brian Badi, Executive Director of MRDA, said: "We don't know for certain when we will be able to resume our work, but we need to be ready.
"There are people depending on us.
"Fighting first broke out in May this year and MRDA was the first to appeal for emergency relief but there was no response.
"To date, no emergency food or non-food items have reached Mundri.
"The people are suffering now and depending largely on wild roots and fruit to survive."