This 2010 Centers for Disease Control and Prevention (CDC) photo shows an "Anopheles gambiae" mosquito, the principal vector of malaria in Africa. (Picture: Reuters/Mary F Adams/CDC)

Nairobi, Kenya – Malaria is killing three children each day in an overcrowded camp sheltering civilians in South Sudan, a medical charity said, as people continue to flee fighting despite an August peace deal that has yet to be felt on the ground.

Malaria is "skyrocketing", with 4 000 patients receiving treatment each week – about 4 percent of the population of Bentiu camp, Medecins Sans Frontieres (MSF) said in a statement.

Malaria cases in the camp, which is in the capital of northern Unity State, were 43 times higher in August and September than at the start of the year, MSF said.

Malaria spikes during the mid-year rainy season as mosquitoes, which transmit the disease, breed in stagnant water.

"The malaria outbreak in the Bentiu camp is unprecedented in scope and has been claiming the lives of far too many children," Vanessa Cramond, MSF's medical coordinator in Bentiu said.

Oil-rich Bentiu has been on the frontline of South Sudan's 20 month-old civil war. As a result of fighting, the number of civilians sheltering in the United Nations (UN) military camp in the town has doubled since May to more than 110 000 people, MSF said.

The world's youngest country descended into civil war in December 2013 when a row between President Salva Kiir and former Vice President Riek Machar spiralled into fighting, reopening ethnic fault lines between Kiir's Dinka and his foe's Nuer people.

One in five of South Sudan's 11 million people have fled their homes as a result of the war, often hiding in the bush without access to bednets, food, water or medical care.

Children are often not brought to MSF's Bentiu clinic until they are in a critical condition, the charity said.

To speed up diagnosis and treatment to save lives, MSF and the UN children's fund (UNICEF) went door-to-door in the camp looking for sick, feverish children. More than 16 000 children under five received malaria treatment during the September 10 to 17 campaign, MSF said.

Mediators say both sides have violated a ceasefire introduced on August 30 after they signed a power-sharing deal under intense international pressure.

Machar, who is set to become first vice president during a three-year transition, has accused the government of attacking his forces in Unity State.

People are continuing to flee. In the first half of September, 18 000 people arrived by foot and canoe in Nyal, a village south of Bentiu in Unity State, the UN said on September 18.

"I would want to go home but I'm not sure it is safe," said Nyawot Ayuen, a widow living in a camp in neighbouring Warrap State.

"I will just wait (until) fighting stops completely."