Cars stop before a flooded area, after Cyclone Batsirai made landfall, on a road in Vohiparara, Madagascar. Reuters

Cyclone Batsirai killed at least 10 people and displaced nearly 48,000 when it struck Madagascar overnight, the second to hit the Indian Ocean island in just two weeks, the national disaster management agency said on Sunday.

One of the worst-hit towns was Nosy Varika on the east coast where almost 95 per cent of buildings were destroyed "as if we had just been bombed" and floods cut access, an official said.

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The cyclone later weakened but not before wreaking havoc in the poor Indian Ocean island nation which is still reeling from a deadly tropical storm earlier this year.

This still image shows trees swaying in strong winds as cyclone Batsirai hits Mananjary, Madagascar. Reuters

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.

Cyclone Batsirai swept inland late on Saturday, slamming into the eastern coastline with heavy rain and wind speeds of 165 kph (100 mph). It was projected it could displace as many as 150,000 people.

Locals stand on a damaged road following a landslide, as Cyclone Batsirai hits Madagascar. Reuters

The damage from the storm compounded the destruction wreaked by Cyclone Ana, which hit the island, with a population of nearly 30,000,000, two weeks ago, killing 55 people and displacing 130,000

Batsirai made landfall late Saturday as an "intense tropical cyclone", packing winds of 165 kilometres (102 miles) per hour, Faly Aritiana Fabien of the country's disaster management agency told AFP.

His colleague responsible for risk management, Paolo Emilio Raholinarivo, listed 10 dead, but gave no further details.

Locals find shelter as Cyclone Batsirai sweeps inland, in Fianarantsoa, Madagascar. Reuters

However the national meteorological office — which had warned of "significant and widespread damage" — said on Sunday that Batsirai had weakened.

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

Some 10,000 people on La Reunion were still without electricity on Sunday, three days after the tropical cyclone passed through the island, injuring 12 people on its path.

Ana affected at least 131,000 people across Madagascar in late January, with nearly 60 people killed, mostly in the capital Antananarivo.