Seventeen people died on Monday, after a house crumbled following a mudslide in the Ivory suburb, south-east of the capital Antananarivo.
"On a national scale, the provisional toll is 29 dead, 22 missing, 17,170 displaced and 83,023 affected," the National Bureau for Risk and Catastrophe Management said in a statement.
The cyclone, which made landfall on Friday morning, lashed the eastern part of the African island off Mozambique with violent winds and heavy rains before moving off the territory on Saturday night.
The cyclone caused flash flooding in the capital Antananarivo and the port city of Toamasina and in the eastern town of Tamatave. Several homes were without power and roads cut off by felled trees.
Madagascar, one of the world's poorest countries, is regularly hit by cyclones.
In March last year, cyclone Enawo killed at least 78 people.
