Cyclone Batsirai killed at least 20 people and displaced nearly 55,000 when it struck Madagascar overnight, the national disaster management agency said on Sunday.

Madagascar was already reeling from a tropical storm which killed 55 people weeks earlier, and the latest extreme weather event came as South African President Cyril Ramaphosa said the continent is "bearing both the brunt and the cost" of global warming.

Parts of the country were lashed with heavy rains and wind before the cyclone made landfall in Mananjary.

It uprooted trees, destroyed buildings and forced residents to weigh down flimsy corrugated iron roofs along its path, AFP correspondents saw.

The rain will cause flooding across parts of the country, Madagascar's meteorological office said on Sunday.

Batsirai made landfall late Saturday as an "intense tropical cyclone," packing winds of 165 kilometers per hour, Faly Aritiana Fabien of the country's disaster management agency told AFP.

The cyclone's average wind speed had almost halved to 80 kmh, while the strongest gusts had scaled back to 110 kmh from the 235 kmh recorded when it made landfall, Meteor Madagascar said.

The World Food Program, citing estimates from national authorities, said around 595,000 people could be directly affected by Batsirai, and 150,000 more might be displaced because of new landslides and flooding.

The storm poses a risk to at least 4.4 million people in total, the International Federation of Red Cross and Red Crescent Societies said.

In 2018, the country suffered a double whammy with Cyclone Ava killing 51 people in January and tropical storm Eliakim leaving 20 people dead two months later.

And in March 2017, at least 78 people perished in Cyclone Enawo.

Global warming has increased the risk of flooding and tropical storms, as the atmosphere retains more water and rainfall patterns are disrupted.

Southern parts of Madagascar are reeling from the worst drought in four decades.