Madagascar has seen at least 41 deaths and 100,000 people have been forced to flee their homes to makeshift shelters.
In Malawi, at least 19 people have died. The country has suffered a nationwide power cut and some areas have been declared disaster zones.
Mozambique, meanwhile, reports more than a dozen deaths.
But officials there say the true number is still unknown, with 20,000 affected by the flooding.
Some 3,000 homes in Mozambique are partially destroyed, and more than 600 are left in total ruin, Mozambique’s national disaster agency estimates.
Prime Minister Carlos Agostinho do Rosário said that his country was not begging for help – but the challenge was bigger than anyone country’s ability to tackle it.
And he pointed to the increasing frequency and intensity of extreme weather events.
“We are a country that does not contribute much to climate change, and yet we are one of the countries that suffer the most from its impact,” he said.
He has called for international aid – and Unicef, the United Nations a children’s charity, said it was deploying staff to the country to help the 45,000 people it estimated will need humanitarian aid.
In Malawi, the floods hit electricity infrastructure as well as homes, leaving beleaguered towns in darkness as the water rose. Power has started to come back for many, after days of blackouts.
“This is devastating. Look, all my maize crop has been buried. I planted one and a half acres. All the crop is gone,” Roben Mphassa, a farmer in the Chikwawa area in Malawi, told Reuters.
“This disaster is the second one I’ve experienced in my life. But this is the worst.”
While Noria Kananji said the storm took the roof off her home and four homes nearby had been destroyed.
Madagascar was the first nation hit, as the storm made landfall on Monday, and has reported the most confirmed deaths. Schools and gyms in the capital, Antananarivo, have been transformed into emergency shelters for the displaced.
“We only brought our most important possessions,” Berthine Razafiarisoa, who took shelter in one with his 10-strong family, told Agence France Press.
Meanwhile, weather services in the region have warned of another storm building in the Indian Ocean, which may materialise in the coming days.
It would be one of several such storms usually expected before the end of the season in two months’ time.
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