It has reported that more than 100,000 people have fled from their homes in the last ten days. This figures adds to the two million people within the country that have been uprooted by civil war since the end of 2013.
The charity is warning that displaced Christians are in urgent need of humanitarian help, but the ongoing fighting means that aid agencies and the UN cannot reach them.
In a statement Rosie Crowther, Christian Aid Emergency Programme Officer said: "Citizens are being caught up in the fighting.
"May is the peak of the planting season in South Sudan, when people need to be able to move freely and safely to tend to their crops.
"This new outbreak of fighting is preventing people from growing the crops they so desperately need and will only exacerbate the ongoing food security situation."
The Christian charity is supporting projects in the southern part of the state to respond to the immediate needs of those most vulnerable.
Rosie Crowther, from the charity, added: "We are working in some of the worst affected areas to meet immediate food needs, provide safe drinking water, and promote safe hygiene and sanitation practices to help prevent the spread of disease.
"In Koch we have been repairing boreholes so that communities can access safe drinking water.
"We are training pump mechanics and water committees to ensure that the boreholes are maintained in the longer term, as well as facilitating hygiene awareness campaigns in schools."
Christian Aid is asking the international community to help provide food, basic items and funding to affected parties.
The current tensions in South Sudan began just over a year and a half ago following a political struggle between President Salva Kiir and former Vice President Riek Machar.
The problems escalated along ethnic lines and spread across the country.
So far tens of thousands of people have died, and Christian Aid anticipates that 6.4 million citizens will need humanitarian aid this year.
