Heavy rains continued to wreak havoc in East Africa Saturday, as floods that have already displaced hundreds of thousands heightened fears of food shortages and disease outbreaks across the region.

In Kampala, Uganda's minister for relief, disaster preparedness and refugees, Musa Ecweru, said high waters had submerged entire villages and destroyed many farms in the east of the country.

"Many people have sought refuge in churches and raised grounds, while others have left the affected areas to live with relatives in other places and food crops in gardens have been destroyed," Ecweru told reporters.

The minister estimated the number of people displaced by the floods to be around 150,000.

"Cholera cases have been reported and we are working with the health ministry to mitigate the problems," he added.

Ecweru said the government would on Monday begin ferrying food to those affected by the floods in eastern regions, better known for the recurrent droughts that normally plague the nomadic pastoralists living there.

The minister gave the example of Abalirela, where the entire population of 30,000 had only recently returned after having been driven off by the 2003 raids of the rebel Lord's Resistance Army (LRA).

"These people had just returned home and started cultivating their own food. The floods have again displaced them and all the food crops are destroyed," Ecweru said.

Neighbouring regions in Kenya have also been affected, with more than 1,000 families displaced after heavy rains in the western highlands caused a river to burst its banks and flood villages.

"More families have been marooned and we are in the process of rescuing them," Anthony Mwangi of the Kenya Red Cross Society told AFP. "No one has died, no one has been injured and everybody has been accounted for."

Mwangi warned that the persistent rains risked causing the river Nzoia to breach another dyke and flood more villages.

In Sudan, six weeks of deluge have directly affected at least 365,000 people, destroyed crops, food stocks, farmlands and livestock, according to the United Nations, which has launched an appeal for funds.

In a statement released on Friday, the UN mission in Sudan said some 150,000 people had been left without shelter, mainly in the south of the country.

Floods affecting several areas of Sudan have so far killed 64 people. On Wednesday, the World Health Organisation said an outbreak of cholera had killed 49 people and affected 700 others in northeastern regions.

The UN humanitarian agency has predicted that the rains will persist until the middle of next month.

In nearby Eritrea, heavy rain in the western lowlands have delayed crop planting and washed away bridges.

In late July, more than 10,000 people had been displaced by heavy rains in western Ethiopia.

Last year, more than 600 people were killed and hundreds of thousands affected by unusually heavy floods that ravaged several regions in Ethiopia.