At least 14 people have been killed in southern Somalia after torrential rains triggered flash floods that have caused havoc in several towns and villages.

Bridges, roads and houses have been damaged or destroyed and many people have been forced to flee their homes in search of safer ground.

In the town of Baardhere in Jubaland state, 14 people were killed including three members of the same family, district commissioner Mohamed Weli Yusuf told reporters.

"Most of the casualties were caused after the victims were trapped across a bridge in the town Thursday evening which was swept up in the floods," he said.

"It was very difficult to rescue these people because of the time the incident happened and the lack of resources in the town."

The rains signal the early start of the April-June rainy season, and have brought some relief to areas of the country suffering from the worst drought in four decades.

But the UN's humanitarian response agency OCHA warned in a statement on Saturday of the risk of an increase in diseases such as cholera as living conditions likely deteriorate.

Baardhere resident Ahmed Omar said there had been heavy rains in the region over the past three days.

"Floods devastated Baardhere town, my house was destroyed and most of my belongings swept away by the flood. Thanks to God my family survived but five people died in my neighbourhood including children and women," he told AFP.

"Now the whole town is under water and most families fled to higher ground," he added.

Jubaland president Ahmed Mohamed Islam on Saturday sent condolences to the relatives of those who lost their lives and called for urgent assistance to be sent to those affected by the disaster.

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.

Earlier this month, the World Health Organization (WHO) warned that nearly 100,000 people in Somalia were facing catastrophic levels of hunger due to the worst drought to hit the region in four decades.

Five straight failed rainy seasons across swathes of Somalia, Kenya and Ethiopia have killed millions of livestock, destroyed crops, and forced more than one million people from their homes in search of food and water.

While famine thresholds have not been reached, the United Nations says more than half of Somalia's population will need humanitarian assistance this year.