Large storms rocked the southern and central areas of the country on Saturday, including the capital, where water eventually stood almost a metre deep in some parts of the city.
Somali media reported six people had been killed by the flooding so far, while hundreds of homes were also thought to have been damaged or destroyed.
The United Nation’s Office for the Coordination of Humanitarian Affairs (OCHA), said the rainfall was the heaviest the country had seen in more than 30 years.
It estimated more than 750,000 people had been affected by the flooding, while damage to infrastructure and cropland had also been widespread.
A new $80m (£59m) appeal has been launched by the UN in a bid to provide short-term relief to the more than 200,000 people thought to have been displaced by the rainfall.
“As climate change risks invariably increase, more resources are needed to address the root causes of fragility, chronic poverty and low human development that are affecting the bulk of the population,” said UN humanitarian coordinator for Somalia, Peter de Clercq.
“The administration continues to provide assistance with the impact of the rainfall,” he wrote on Twitter: “We ask citizens to take part in the rescue to help victims.”
“I thank the public and the military for providing assistance to Mogadishu for the impact of rainfall.”
Flooding comes against the backdrop of an on-going humanitarian effort to provide aid to millions of people in the country hit by several consecutive drought seasons.
The first half of Somalia’s rainy season, which began in March, recorded unprecedented levels of rainfall only comparable with storms seen in Somalia in 1981, experts said.
Heavy rains across the country and in the Ethiopian highlands have caused the Juba and Shabelle rivers to burst their banks, causing flash flooding in some areas.
OCHA warned more devastation is likely to take place if heavy rains continue, although the full impact of the flooding had yet to be established.
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