Thousands of stagnant pools of waters, and piles of rubbish and dead animals around houses, have prompted the warnings.
The situation is compounded by the absence - and in some cases the destruction - of sanitary and piped water networks, as well as the lack of equipment and technical expertise.
Swarms of flies and mosquitoes are in evidence in urban areas, and swamps have developed which are mixed with sewage.
"Flooding damaged the sewage and water supply system and has created swampy areas; piles of rubbish are strewn around," Alabd Rubia Bamusa, the head of Mukalla's health department, told IRIN.
Where water networks have yet to be repaired in Mukalla, some families have been lucky enough to have their water trucked in by local charities. In rural areas many of the wells have been contaminated. The lack of clean drinking water poses a risk to health, especially among children.
The diseases most likely to cause problems are malaria, cholera, polio, and acute diarrhoea, according to Adel al-Hitar, an official at Mukalla's health department.
Adnan Bajunaid, head of the health committee at the Charitable Society for Social Welfare (CSSW) in Mukalla, said diarrhoea, respiratory infections and fever had already appeared among flood victims, especially displaced families.
Polio might resurface if vaccination teams were unable to reach children in affected areas, he added.
Health experts said epidemics could spread if swamps and flood debris are not tackled within 15 days - and 11 days have now passed since these hazards were created.
"UNICEF's [The UN Children's Fund's] major concern is to save children who, due to the high incidence of malnutrition, are highly vulnerable to the water-borne diseases that loom large after the flood has receded," said Aboudou Karimou Adjibade, a UNICEF representative.
In a 2 November statement UNICEF said the floods had left 98 dead and thousands displaced, with women and children at high risk of contracting water-borne diseases and being exposed to harsh winter weather. Around 3,264 households were destroyed. Over 22,000 displaced people have taken shelter in 65 schools.
UNICEF said it had sent an aid convoy to help children and families hit by the floods. The assistance included jerry cans, storage tanks for drinking water and essential hygienic kits that children and families need in crowded temporary shelters.
Bamusa of Mukalla's health department said the authorities had begun removing flood debris and spraying swamps with insecticides.
CSSW on 4 November also started spraying swampy areas, and its teams had distributed medicines to displaced families.