Heavy rains that triggered flash flooding in the troubled Horn of Africa nation have driven around half a million people from their homes and more than 30 people have perished, according to the government.
The UN's World Food Programme said the flooding has devastated communities already struggling to recover from the worst drought in four decades that sent millions to the brink of starvation.
While humanitarian aid staved off famine, the WFP said Somalia is still facing the highest levels of hunger it has suffered in over a decade.
However, the WFP said significant funding shortfalls meant it can only provide food assistance to under half of the people most in need.
"But with a quarter of Somalia's population -- 4.3 million people -- forecast to face crisis-level hunger or worse... by the end of the year, the support of the humanitarian community remains a lifeline," it added.
"The end of over two years of drought that pushed the country to the brink of famine has brought little relief for families."
The UN humanitarian agency, OCHA, last week said Somalia was facing "once-in-a-century flooding" and warned that 1.6 million people could be affected.
Somalia is considered one of the most vulnerable countries to climate change but is particularly ill-equipped to cope with the crisis as it battles a deadly Islamist insurgency.
The country has been battered by unrelenting downpours since the beginning of the month linked to the El Nino weather pattern.
The bulk of destruction is in Gedo region, southern Somalia, and central Hiran region where the seasonal Shabelle River broke its banks, submerged roads and washed away properties in Beledweyne town.
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