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More than a million people have been displaced in Somalia after the country was hit by severe flooding caused by torrential rains, the president said.

Somalia and its Horn of Africa neighbours Kenya and Ethiopia are battling flash floods caused by heavy rainfall linked to the El Nino weather pattern.

The floods are exacerbating the humanitarian crisis in the region just as it emerges from the worst drought in four decades that left millions of people hungry.

"My brothers, our country is in a critical state and our people have been affected by the flooding everywhere," President Hassan Sheikh Mohamud said on Wednesday evening.

He said that 101 people had died in the flooding.

Authorities in Mogadishu declared a state of emergency this month over the disaster, and have warned against the proliferation of disease.

In neighbouring Kenya, around 120 people have died in heavy flooding and more than 89,000 households have been displaced, according to the interior ministry.

Another 57 people have died in Ethiopia as a result of the floods, heavy rainfall and landslides, according to the UN's humanitarian response agency OCHA.

The Horn of Africa is one of the regions which is most vulnerable to climate change, and extreme weather events are becoming increasingly frequent and intense.

Action Against Hunger said the current situation was "dire".

"Regions that were struggling to recover from the economic and environmental impacts of prolonged drought are now doubly burdened with flooding," the charity said.