Floods have killed at least 96 people, the country's Council of Ministers said Thursday.
Among the worst hit towns is the densely populated Beledweyne, where the Shabelle River has burst its banks, destroyed many homes and caused thousands to flee to higher ground near the border with Ethiopia.
Hakima Mohamud Hareed, a mother of four children including one who is disabled, said that her family constantly looks for shelter.
The family recently moved to Beledweyne, fleeing battles between the extremist group al-Shabab and Somali government forces.
"We left our home in search of safety and stability, but little did we know that we would end up facing another calamity," she said.
In the displacement camp of Kutiimo in Beledweyne, the floods destroyed the family's small, tattered tent. Wind lashes the damp and flimsy fabric.
"The floods washed away all our belongings, so we were left only with our lives," she said.
"It was a traumatic experience for all of us."
They aren't alone. According to the humanitarian group Save the Children, the flooding has forced an estimated 250,000 people, or 90 per cent of Beledweyne's population, out of their homes.
Somalia's federal government declared a state of emergency in October after extreme weather exacerbated by El Niño destroyed homes, roads and bridges.
An El Niño is a natural, temporary and occasional warming of part of the Pacific that shifts weather patterns across the globe, often by moving the airborne paths for storms. It hits hardest in December through February. Scientists believe climate change is making El Niño stronger.
Many parts of Somalia, as well as in neighbouring Horn of Africa nations Kenya and Ethiopia, are still receiving torrential rainfall in what aid agencies have described as a rare flooding phenomenon.
The United Nations-backed Somali Water and Land Information Management project has warned of "a flood event of a magnitude statistically likely only once in 100 years," the UN food agency said in a recent statement.
About 1.6 million people in Somalia could be affected by flooding in the rainy season lasting until December, it said.
Beledweyne, in the central region of Hiran, may be the most devastated community. As floodwaters swept through, homes were washed away.
Hakima said that her family may be safe from flooding in their camp, but they are hungry and desperate for warm shelter.
"We ask our Somali brothers and sisters to help us get out of this situation, as we are struggling to survive," she said.
Mukhtar Moalim, the owner of a retail shop, described frantic attempts to save his property in Beledweyne's market after the river burst its banks. He and a relative swam towards the shop to try to prevent the water from flowing in, putting concrete blocks against the door.
But the water level keeps rising, also threatening their residence on the floor above the shop from which they monitor the destruction.
At least 53 people have been killed by flooding across Somalia, said Hassan Issee, who manages emergency operations at the Somalia Disaster Management Agency.
"The situation is grave, and we are doing our best to provide relief to the affected people," he said.
Mogadishu, the Somali capital, has also been affected. The city's main streets, including the road to the airport, have flooded.
Speaking on Wednesday in the Dollow district of Gedo region, where many families have been displaced by flooding, Prime Minister Hamza Abdi Barre urged the international community to help.
"We are doing our best, but we need more support," he said.
