Tropical Cyclone Emnati is the fourth tropical storm, in as many weeks, to hit the island of Madagascar.
Brian Lander, deputy director emergencies operations for the United Nations World Food Programme, says "we need to think about how they are going to adapt to this new reality for them."
The storm, which passed just north of the Indian Ocean islands of Mauritius and Reunion, had weakened slightly by the time it reached the eastern coast of Madagascar.
But it was still packing winds of around 100 kilometres per hour (62 miles per hour) and gusts of 140 kph, according to Meteo-France.
The cyclone is forecast to exit Madagascar Wednesday night, but national weather forecaster Meteo-Madagascar warned of strong gusts, heavy rain and widespread flooding around the southern and southeastern districts.
Meteo-France has warned that another tropical storm may form in the next five days.
UN agencies had on Tuesday said they were preparing "for the worst".
Another storm, Cyclone Batsirai, struck the island on February 5, affecting some 270,000 people and claiming 121 lives.
At the same time, some 21,000 people remain displaced from when Tropical Storm Ana struck in late January.
Another 5,000 were affected last week by Tropical Storm Dumako.
More than 37,000 people have been moved to emergency shelters as a precautionary measure.
One of the poorest countries in the world, Madagascar's southern region has been ravaged by drought.
The UN says it is the worst in 40 years and blames climate change for the crisis.
Madagascar is prone to numerous storms and cyclones between November and April every year.