National disaster management office in Madagascar (BNGC) made the announcement on Friday, saying that 38 people had been killed countrywide by tropical cyclone Enawo and an estimated 53,000 people displaced by storm waters.
It is expected the death toll could be significantly higher in the days to come.
Thierry Venty, Executive Secretary of the National Bureau of Risk and Disaster Management, said on national television that those killed included victims of landslides caused by the storm. Another 116,191 people have been displaced or had their property damaged, he said.
A category 4 hurricane, cyclone Enawo was recorded at 230 kilometres per hour when it made landfall in the Antalaha area - northeast of the country.
Enawo hit Madagascar's remote northeast on Tuesday, swelling rivers to bursting point and sparking fears of widespread flooding.
Images and videos on social media showed flooded roads and corrugated sheeting ripped from roofs.
The Red Cross says 700 000 people could be affected by the cyclone, the relief aid organisation deployed 500 volunteers there yesterday.
It has weakened since making landfall and has now been reclassified as a tropical depression that is moving southwards, away from the island.
In 2012, tropical storm Irina and tropical cyclone Giovanna claimed more than 100 lives in Madagascar. Madagascar has been grappling with severe drought and food shortages since 2015, although storms mostly affect the more affluent northern regions.