There were no immediate reports of deaths or injuries, but local authorities reported extensive damage to houses and other buildings in at least one city.
Cyclone Emnati has crashed into Madagascar's southeastern coast, ripping roofs off houses and raising fears of flooding in a region battered by another tropical storm just weeks ago.
Emnati made landfall early on Wednesday in Manakara Atsimo district, with average sustained winds of 135 kilometres per hour (84 mph) and gusts as strong as 190 kph (118 mph).
There were no immediate reports of deaths or injuries, but local authorities reported extensive damage to houses and other buildings in at least one southeastern city.
Madagascar's National Office for Risk and Disaster Management estimates more than 250,000 people could be impacted by the cyclone. Over 30,000 people have been moved to safety.
The Emnati system had weakened as it worked its way over the Indian Ocean toward Madagascar, the meteorology department said, but it warned that flooding was still likely.
Six regions in the southeast are on red alert, most of them already hard-hit by Cyclone Batsirai early this month.
Emnati is expected to cross the southeastern part of Madagascar and spin out to sea again, meaning it should miss mainland Africa, where previous cyclones have caused deaths and destruction.
Batsirai left more than 120 people dead and displaced 143,000. It destroyed or damaged over 20,000 houses.
Madagascar, an island off the east coast of Africa renowned for its wildlife and unspoiled natural treasures, has now been hit by four major tropical storms in the last month.
They killed nearly 200 people already and compounding issues of food insecurity.
A drought in the south of the country left around 400,000 at risk of starvation last year, according to the UN World Food Programme.