The national disaster management agency BNGRC said the majority had died in Ikongo district, near the east coast of the Indian Ocean island.
About 125,000 people have been affected after Batsirai struck last weekend, the agency said in an updated fact sheet.
Aid agencies are worried about ensuring clean drinking water, and have begun setting up purification systems. Water-borne diseases pose a major health risk after tropical storms.
Madagascar is one of the poorest countries in the world. Some 42 percent of children suffer from chronic malnutrition, even without a natural disaster.
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