Cyclone Fytia, packing gusts of up to 210 kilometres (130 miles) per hour, hit the Indian Ocean island early on Saturday and left early Sunday.
One of the seven people confirmed dead was killed in the capital, Antananarivo, while another person was still missing after being swept away by a swollen river, the BNGRC disaster management agency said.
More than 20,000 people had to leave their homes, it said.
Fytia was the fifth tropical storm to hit Madagascar since September, according to the meteorological agency. The region's cyclone season typically ends in March or April.
The country is particularly exposed to extreme weather events such as storms and droughts which experts say are expected to worsen with climate change.
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