Officials said on Monday the flood was caused by heavy rains at the weekend which led the Wabe Shebell river to burst its banks.
An official said the toll was expected to rise as the river burst its banks at night while many people were sleeping.
"Many are still hanging on to trees for dear life," said Muhammad Adme Abdi, district administrator of West Emi in Ethiopia's Somali state, about 840km from Addis Ababa.
Officials from government agencies, the United Nations and relief organisations were meeting on Monday to plan relief operations.
Their efforts, however, will be complicated by rampant insecurity which makes road travel without a military escort impossible.
Before the flooding, the area had been repeatedly hit by drought.