Bridges and roads have been destroyed by the downpour, making it difficult to reach affected households, the Somali Regional State Communication Bureau said in a statement, with damage to livestock, crops and property also reported.
"More than 20 people have died in the flood so far... more than 12,000 families have been displaced," the statement said.
"Rising rainfall and forecasts show that the risk of flooding remains high."
The UN's humanitarian agency, OCHA, said last month that eastern Africa would likely encounter heavier than normal rains over the October-December period because of the El Nino phenomenon.
El Nino is a naturally occurring pattern associated with increased heat worldwide, as well as drought in some parts of the world and heavy rains elsewhere.
Since the start of the October-December monsoon in Somalia, "floods due to heavy rains have affected at least 405,652 people, with 14 deaths", OCHA said in a situation report released on Saturday.
"At least 47,100 people have relocated to higher grounds to avoid the risk of flooding," the agency said, adding that the downpour had cut off access to markets and farmland in some areas.
The Horn of Africa is one of the regions most vulnerable to climate change, and extreme weather events are occurring with increased frequency and intensity.
Since late 2020, Somalia as well as parts of Ethiopia and Kenya have been suffering the region's worst drought in 40 years.
At the end of 2019, at least 265 people died and tens of thousands were displaced during two months of relentless rainfall in several countries in East Africa.
The extreme downpours affected close to two million people and washed away tens of thousands of livestock in Burundi, Djibouti, Ethiopia, Kenya, Somalia, South Sudan, Tanzania and Uganda.
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