Cyclone Belna was expected to hit northwestern Madagascar on Monday after brushing past the Indian Ocean island of Mayotte and the Comoros archipelago.
Officials in Madagascar issued a red alert for the western Boeny region, projecting that the tropical cyclone would make landfall on Monday afternoon.
The cyclone has already begun lashing the area, reaching a maximum wind speed of 165km per hour, the UN Office for the Coordination of Humanitarian Affairs (OCHA) said.
An emergency operations team has been deployed to the Boeny region, which includes the major port city of Mahajanga, and all schools along the western coast have been closed.
People living in flood-prone areas of the impoverished island nation are being evacuated "as a preventative measure", OCHA said.
Cyclone Belna bypassed Mayotte on Sunday after initial forecasts put the French island in its direct path.
Neither Mayotte nor the Comoros are reported to have suffered significant damage.
Madagascar, a former French colony off Africa's southeastern coast, is regularly hit by cyclones and other tropical storms.
Cyclone Ava killed 51 people in January last year, and two months later tropical storm Eliakim displaced around 19,000 inhabitants.