Across Kenya, Rwanda and Somalia, the death toll from the flooding has surpassed 400, with many thousands more forced to flee their homes to escape rising waters.
Rwanda's Ministry of Disaster Management puts its death toll at just over 200 in a period of four months.The number includes 18 killed this month as a result of landslides triggered by heavy rains.
In Somalia, the Juba and Shabelle rivers have burst their banks.
Justin Brady, head of the U.N. Office of Coordination of Humanitarian Affairs in Somalia, said the situation has left those affected by the flooding vulnerable to malnutrition and disease.
"We have had a number of deaths reported at different junctures in the flooding.," he said "I believe right now we are looking at about 220,000 people who are temporarily displaced due to the flood waters and until those recede, those people will remain displaced and in need of humanitarian assistance. We may see that number climb up in the short term with flooding spreading down stream as flood waters move towards the Indian Ocean."
Earlier in the week, at least 15 people died in Somaliland when heavy rains caused by tropical cyclone Sagar swept through the Horn of Africa. The cyclone system has caused heavy rains in both the Puntland and Somaliland regions of Somalia, and then moved along the coast to Djibouti.
Brady said those areas were especially hard-hit by drought the last three years.
"So you already had a very low level of resilience of the population," he said. "There are several districts that were most affected. The government is continuing to refine the number of people in need and initially it was around 670,000. That number has come down as I understand, but it's a case of being able to get into areas."
In Kenya, the Red Cross said at least 200 people have died as a result of the heavy rains. In the biggest catastrophe, a dam burst last week on a commercial farm in the Rift Valley, killing at least 48.
Emergency appeals have been launched by the affected governments and NGOs for humanitarian assistance.