Flooding and strong winds caused by a tropical cyclone left at least 18 people dead and thousands homeless across two countries in the Horn of Africa, an aid agency said Monday.

Cyclone Sagar formed last week in the Gulf of Aden off Yemen's coast and made landfall on Saturday in Djibouti and Somaliland, a breakaway state in northern Somalia where the bulk of the deaths occurred.

"1,780 families fled their homes due to the storm, 16 people were reported killed, and at least 80 homes were destroyed," Norwegian Refugee Council (NRC) said in a statement, citing the UN's humanitarian coordinator OCHA.

The aid group added that the storm left two people dead in Djibouti's capital and flooded several neighbourhoods, affecting between 20,000 and 30,000 people.

"This is the biggest storm to hit the region in years," NRC regional director Nigel Tricks said.

The United Nations Office for the Coordination of Humanitarian Affairs (OCHA) said the full extent of the damage in Somaliland remained unclear because the storm destroyed roads and communication infrastructure.

Forty fishermen who were at sea and were not warned about the storm remain unaccounted for, the body added.

Relief efforts have been hindered by deadly clashes that erupted last week in a disputed desert region between Somaliland and the semi-autonomous Somali state of Puntland.

Those clashes displaced 10,000 people and "further (complicated) an already complex humanitarian picture," OCHA said in a statement on Sunday.

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