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.
Cyclone Batsirai swept inland late on Saturday, slamming into the eastern coastline with heavy rain and wind speeds of 165 kilometres per hour.
It was projected it could displace as many as 150,000 people.
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.
Madagascar's office of disaster and risk management said in a bulletin late on Sunday 10 people had been killed.
State radio said some died when their house collapsed in the town of Ambalavao, about 460 km south of the capital Antananarivo.
"We saw only desolation: uprooted trees, fallen electric poles, roofs torn off by the wind, the city completely under water," Nirina Rahaingosoa, a resident of Fianarantsoa, 420km south of the capital, told Reuters by phone.
Electricity was knocked out in the town as poles were toppled by the strong gusts of winds that blew all night into Sunday morning, he said.
Willy Raharijaona, technical advisor to the vice president of Madagascar's Senate, said some parts of the southeast had been cut off from the surrounding areas by flooding.
"It's as if we had just been bombed. The city of Nosy Varika is almost 95 per cent destroyed," he said.
"The solid houses saw their roofs torn off by the wind. The wooden huts have for the most part been destroyed."
Another resident who gave only one name, Raharijaona, told Reuters even schools and churches that had been preparing to shelter the displaced around Mananjary town in the southeastern region had their roofs torn off.
Elsewhere, in the central Madagascar region of Haute Matsiatra, villagers shovelled mud from a road on Sunday to clear damage from a landslide caused by Batsirai.
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