The second storm in Cyclone Batsirai weeks destroys homes as it makes landfall
Gusts of up to 250km/h (155mph) are forecast and wave up to 15m high.
Many people have been moved to shelters, and local officials fear that landslides and flooding could leave tens of thousands more homeless.
Storm Ana caused widespread destruction when it hit the Southern African island nation last month, killing 55 people.
Cyclone Batsirai made landfall at around 20:00 local time (17:00 GMT). Just one hour later, nearly 27,000 people had been displaced from their homes, according to the country's disaster management agency. There were reports of power outages, destroyed homes and fallen trees.
"The winds are terrible. I've never experienced this...The waves are very high," said Hanitra Raharisoa, a resident of Mananjary, a coastal town close to where the storm hit.
Further up the coast, 200 people had crammed into one room in a concrete building in the town of Vatomandry, hoping the relatively sturdy structure would keep them safe.
Clean water is scarce in the town after the utility company switched off supplies ahead of the storm, prompting fears of illness caused by dirty water.
"The government must help us. We have not been given anything," said community leader Thierry Louison Leiby.
The UN World Food Programme (WFP) has prepared food stocks to distribute to those in need, while some people have already been evacuated. The UN has put rescue aircraft on standby.
Experts fear that Cyclone Batsirai could be even more powerful than Storm Ana, which also hit Mozambique, Malawi and Zimbabwe.
Heavy rainfall and high waves are raising the spectre of flash floods as the ground is already saturated.
Environment Minister Vahinala Raharinirina told that it could be the worst cyclone to hit the island for 17 years, affecting some 600,000 people in total.
The WFP says the recent pattern of destructive storms caused by global warming and climate change has caused loss of harvest, high food prices and increased food insecurity in the region.
"The people of Southern Africa have been on the front lines of climate extremes for many years now and each passing storm sets them back, resetting the progress made," said senior WFP official Margaret Malu.
Experts say that extreme weather events like cyclones will become more frequent because of climate change.
Madagascar is also just recovering from the effects of an extreme drought, which was also blamed on global warming.
Ms Raharinirina said that the country had submitted a plan to the COP26 climate conference, which showed it needed $1bn (£740m) a year to adapt to the effects of climate change.
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