Some 20,000 people have been affected by the flooding mainly in the provinces of Antananarivo and Fianarantsoa. Most of the deaths were caused by the collapse of houses.
"It is normal for the country to receive rain at this time of the year, but since the beginning of January the quantity of rain recorded has already reached 550 mm, two times the average level of rains that usually fall during the whole month," UNDP programme officer Michel Matera told IRIN.
UNDP said many of the poorest, low-lying neighbourhoods in the affected regions were flooded and that the risk for epidemics was high.
"Despite the risk of flooding, many people refuse to evacuate from the low-lying areas. The harvest season (rice) was to begin in a few weeks in the areas of Antananarivo and the losses are likely to be important [significant] if immediate harvest is not done," UNDP noted in its latest situation report on the flooding.
Although the government has not yet declared a state of emergency, authorities last week launched an emergency plan for the capital city, Antananarivo.
Matera said essential relief items such as tents, blankets and medicine for malaria and diarrhoea were needed.
According to the country's meteorological department the downpour is expected to continue for a few days.
Before the heavy rains, Madagascar was already struggling to cope with the aftershocks of a political crisis that left thousands of people unemployed.
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