By Tom Miles

GENEVA (Reuters) - Dozens of people have fallen ill with suspected cholera in South Sudan's capital of Juba, while a U.N. food warehouse was looted and destroyed, incurring $20 million of damage, the United Nations said on Tuesday.

"We expect a huge humanitarian crisis. Even before the current crisis, the health system in South Sudan was facing a crisis due to near economic collapse," World Health Organization spokeswoman Fadela Chaib said.

Cholera is a type of acute watery diarrhea which kills fewer than 1 percent of sufferers if there is proper treatment with oral rehydration salts, according to the World Health Organisation.

But conditions in Juba, where fighting erupted on July 7 between forces loyal to President Salva Kiir and those loyal to his deputy, Riek Machar, are far from ideal, the International Organization for Migration (IOM) says.

The fighting uprooted about 36,000 people who sought shelter at U.N. compounds, and 14,900 are still displaced, IOM said.

Other parts of the country have subsequently reported clashes, and the U.N. has recommended aid agencies reduce staff in hotspot locations.

Over 5,000 people fled to Uganda, almost all women and children who had walked for days, the U.N. refugee agency UNHCR said.

The violence in Juba prompted many traders and markets to shut down, and insecurity along supply routes meant food supplies were likely to dwindle further, the U.N.'s World Food Programme (WFP) said.

South Sudan has 4.8 million people who are severely short of food, and about 1.6 million people who have been displaced since a civil war broke out in December 2013. A further 743,000 have fled the country, a number the U.N. expects to reach 1 million in the coming months.

WFP lost 4,500 tonnes of commodities as well as vehicles, fuel, office and IT equipment when its warehouse was looted. The losses included specialized foods aimed at reducing "unprecedented" rates of malnutrition.

Two U.N. aircraft were also damaged in the fighting.

WFP is now considering moving food stocks to safe locations and airdropping food to some areas outside Juba, but the government is restricting its helicopter movements.

The U.N. Food and Agriculture Organization also said seeds and tools had been looted from its warehouse, just weeks before harvesting of the main maize and sorghum crop and a second planting season.

IOM, which is mapping potential disease hotspots and setting up oral reydration stations, has a health care clinic at Tong Ping, where one suspected cholera case was identified on July 16. IOM teams are building additional latrines.

"As more people continue to arrive at the site, concerns are increasing over the impact of the rainy season and the spread of other waterborne diseases. Without proper drainage, the rainy season can lead to flooding and extremely muddy conditions for IDPs (internally displaced persons)," an IOM statement said.

Chaib said estimates of the suspected number of cholera victims ranged from about 30 to 70, including six or seven deaths, but laboratory confirmation of the disease was pending.

(Reporting by Tom Miles; Editing by Stephanie Nebehay and Catherine Evans)