A truck is pictured in a village deserted after a cyclone hit it in Yemen's Socotra island.

Reuters/Aden

Winds and rain from the second rare cyclone to hit Yemen in two weeks have killed 13 people, including three children, on Yemen's Socotra island, the fisheries minister said on Tuesday.

Cyclone Megh slammed into Socotra on Sunday with category four hurricane-force winds, and arrived on the Yemeni mainland's southern shore near the port city of Aden on Tuesday.

Fisheries Minister Fahd Kafayen said that three fishermen were also missing on the island, according to his Facebook page.

The storm injured an estimated 60 people and damaged houses, the main power station and hospital on Socotra, the UN humanitarian office OCHA said.

It is an area of the Arabian Sea where cyclones were virtually unheard of before this month, but two such storms have battered Socotra within the past two weeks.

The lack of experience with cyclones means that Yemen, which has been ravaged by war this year, is ill-equipped to deal with floods and high winds.

The latest storm weakened significantly after reaching mainland Yemen's mountainous terrain on Tuesday, about 70 km east of the port of Aden, a spokeswoman for the World Meteorological Organisation (WMO) said.

The Geneva-based organisation said a third storm could be brewing in the Arabian Sea, but spokeswoman Clare Nullis said those winds were expected to abate.

The WMO said the highly unusual strike by two cyclones in a week was due to the "Indian Ocean dipole", a weather phenomenon similar to a regional "El Nino" effect caused by unusually warm surface water in the Arabian Sea.

Megh came a week after Cyclone Chapala killed 11 Yemenis on Socotra and the mainland, dumping nearly a decade of average annual rainfall on the impoverished country in just two days.

More than a third of Socotra's population, 18,000 people, were displaced by that cyclone.

Megh tracked further south than Chapala and, earlier, brought three times the annual rainfall to parts of Puntland in Somalia, threatening flash floods around the tip of the Horn of Africa, the UN Food and Agriculture Organisation said.

Aid efforts in Yemen are hampered by the seven-month war between a Shia Muslim militia based in the capital Sanaa in the north of the country and forces loyal to the exiled government, backed by Gulf Arab states.