NAIROBI (Thomson Reuters Foundation) - Thousands of lives are at risk across South Sudan as massive drug shortages have forced many medical centers to close, a charity said, calling on donors to restore supplies before the deadly malaria season resumes.

A quarter of 42 clinics visited by teams from Medecins Sans Frontieres (MSF) in Aweil, in Northern Bahr el Ghazal, had closed because they did not have essential medicines.

A further half were sending patients to buy their own drugs.

"(A) preventable medical emergency is unfolding," MSF's international president Joanne Liu said in an open letter on Thursday.

"Drug outages are now a reality around the country."

Two in ten South Sudanese have fled their homes since civil war broke out in 2013 in the world's youngest nation following a political dispute between President Salva Kiir and his former deputy, Riek Machar.

The two leaders signed a preliminary peace deal in August and Kiir re-appointed Machar as vice president in February but the conflict has continued.

Drug shortages became a serious problem when a donor project, called the Emergency Medicines Fund, ended in June 2015 and responsibility for procurement reverted to the government, MSF said.

South Sudan's economy has taken a hammering during the war and its currency has weakened dramatically, forcing the government to lay off staff at its embassies across the world.

Oil revenues, which finance 98 percent of South Sudan's budget, have dropped due to falling production and world prices.

Healthcare services have been predominantly funded by charities since independence in 2011.

MSF called for renewed donor funding ahead of the mid-year rainy season when mosquitoes, which transmit the disease, breed in stagnant water.

South Sudan experienced an unprecedented malaria outbreak in 2015, worsened by shortages of anti-malarial drugs, MSF said.

"A new rainy season is approaching fast, promising new outbreaks as well as complicated logistics," Liu said.

"Failure to come together will put the lives of thousands in jeopardy."

(Reporting by Katy Migiro; Editing by Alex Whiting; Please credit the Thomson Reuters Foundation, the charitable arm of Thomson Reuters, that covers humanitarian news, women's rights, trafficking, property rights and climate change. Visit http://news.trust.org to see more stories.)