Cyclone Enawo killed 38 people, injured 180 others and displaced 53,000 after it slammed into Madagascar earlier this week, the national disaster management agency said Friday.
The toll issued by the BNGRC agency was significantly higher than the earlier estimate of just four deaths and 10,000 people displaced issued on Thursday.
More than 32,000 people have been affected in the capital city Antananarivo alone, the agency said in an emailed statement.
Enawo hit Madagascar's remote northeast on Tuesday, swelling rivers to bursting point and sparking fears of widespread flooding.
It has weakened since making landfall and has now been reclassified as a tropical depression which is moving southwards, away from the island which lies 250 miles (400 kilometres) off the coast of Africa.
Videos on social media showed flattened trees, flooded roads and corrugated sheeting ripped from roofs after the cyclone struck.
Up to 700,000 people could be affected by the cyclone which was the most powerful to strike the island since 2012, according to the Red Cross.
The group has deployed 500 volunteers to help the 116,191 people who are known to have been affected by the storm.
In 2012, tropical storm Irina and tropical cyclone Giovanna claimed more than 100 lives.
The Indian Ocean island has suffered severe drought and food shortages since 2015, with the southern region the worst affected.