CAFOD partners report that on September 17 rebels attacked and looted property and churches in Bangbi, Bayote and Duru.
The Catholic Church in Duru was ransacked, three priests were tortured, and 50 of the seminaries students were taken prisoner.
Major town attacked
At the beginning of November, reports came in that the major town in Northern DR Congo - Dungu - which is about 50 miles from the Sudan border had been attacked, causing a further influx of refugees into Sudan, mainly women with young children and the elderly.
The refugees have lost all their household goods, such as cooking utensils, blankets, mosquito nets, cloths and of course shelter. They are in desperate need of basic support
Fr Galdino SakondoCAFOD partner Father Galdino Sakondo, development co-ordinator for the Diocese of Tombura and Yambio towns in South Sudan, says: "In September they started looting property, abducting children, killing civilians and burning villages.
"Populations have crossed borders to escape, causing a refugee crisis in three neighbouring countries; Sudan, Central African Republic and Uganda.
"The refugees are mostly agriculturalists, growing ground nuts, maize, rice and cassava. Some came to Sudan; others went south to Dungu, deeper into Congo.
"The survivors told us that they counted 200 bodies rotting on the road, caught as they tried to flee south. Those that came to Sudan walked more than 20 miles through thick forest."
CAFOD and other Caritas Internationalis agencies have conducted an assessment mission to gauge the scale of the crisis and have provided money to the Diocese of Tambura & Yambio, who will be able to support the refugee population with medical and health care as well as household kits, such as pots, pans and blankets.
Father Galdino continues: "Many arrive in need of medical attention. They have nothing at all, and are dependent on the generosity of host families.
"The refugees have lost all their household goods, such as cooking utensils, blankets, mosquito nets, cloths and of course shelter. They are in desperate need of basic support."
According to UNHCR, the United Nations refugee agency, more than 5,000 refugees have been counted crossing into Sudan.
Catholic church groups also report seeing 60 or more people arriving every day, while more people are said to have taken refuge in the dense bush on the Congolese side.
These latest refugees have put a heavy burden on Western Equatoria, which is already struggling to reintegrate its own people returning after being displaced in Sudan's civil war, which ended in a peace deal three years ago.