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More than 6,000 people were displaced by the storm, called Eliakim, the National Office of Risk and Disaster Management said in a statement late on Sunday.
The tropical storm hit the island's Mananara region, 635 km north-east of Antananarivo, on Saturday night and had a wind speed of 85 km per hour and gusts of 120 km per hour.
In January, the island's disaster management office said Tropical Cyclone Ava killed 51 people.