Some 96,000 people were forced to flee their homes after the Shebelle river burst its banks, flooding lowland areas of Ethiopia's Somali region.
Mines Minister Mohamoud Dirir Gheddi told the BBC on Wednesday that the government was unable to cope with the problem.
"For the last two years people have been praying for rain... Very unfortunately according to what I have seen... villages have been virtually submerged.
"Houses have been destroyed... People have fled to the mountains... they have been left with virtually nothing," he said.
Rescue workers are operating in the area, providing the people with medical supplies, plastic shelters and cooking equipment.
The towns of Kelafo and Mustahil have reportedly been hardest hit by the flooding.
A senior representative of the UN children's fund Unicef, Marc Rubin, said the situation was "very serious and worse than any year before".
"We are very concerned about the humanitarian situation. They have no food, no clean water and the health service has been destroyed," he told the UN information agency Irin.
Food shortages
At least five health centres and two schools have been destroyed, and dozens of villages have been cut off.
The area has been receiving food aid due to the severe drought that has hit some 12.6 million people in the country.
The UN's World Food Programme, which is in Kelafo, has warned that food needs may have to be reassessed because of the flooding.
"Flooding is needed in the area for flood-recession agriculture, but there will be an immediate negative impact on the population," said a WFP representative quoted by Irin.
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