The outbreak at the town of Yei is "under control" but continues to rage in the regional capital Juba where 100-150 new cases are reported each day, down from a peak of 400 new cases a day, according to the United Nations agency.
"There is still a huge epidemic in Juba. We are also concerned that cholera has spread to areas surrounding the two towns," Claire-Lise Chaignat, WHO's global cholera coordinator, told Reuters.
Cholera, an acute intestinal infection spread by contaminated water or food, causes vomiting and acute diarrhoea that can lead to dehydration and death within 24 hours.
The WHO and other aid agencies are helping Sudanese authorities by providing anti-biotics and chlorination tablets, but stocks must be replenished, according to Chaignat.
Two-thirds of south Sudan's population drinks unsafe water. After a 2005 peace deal which ended Africa's longest civil war in Sudan's south, hundreds of thousands of people have been returning home.
The International Federation of Red Cross and Red Crescent Societies -- the world's largest relief network -- appealed on Friday for 1 million Swiss francs ($879,000) to respond to the outbreak over the next three months.
"The region is a transit area for displaced people returning to their homes and 5,000 of them are staying in a camp outside Juba. Densely populated areas, such as this camp, are of particular concern," the Geneva-based group said in a statement.