"Sixty-six people have died in Malawi, 93 injured and 16 people are missing due to Tropical Cyclone Freddy," tweeted the Red Cross which is helping with search and rescue operations.
Earlier, Malawi police spokesman Peter Kalaya told Reuters that the number of people killed and missing because of Freddy was likely to grow as it had affected 10 districts and so far numbers were only in for Blantyre.
He said rescue teams were looking for people in Chilobwe and Ndirande, two of the worst affected townships in Blantyre, where it was still raining on Monday and most residents were without power.
"Some missing people are feared buried in rubble and our team is working with other cooperating national agencies," Kalaya said.
Freddy, now the longest-lasting tropical system every recorded, pummeled Mozambique for the second time in a month as a cyclone over the weekend before weakening as it moved inland towards Malawi.
Mozambique has received more than a year's worth of rainfall in the past four weeks, and there has been concern that Freddy could cause rivers to burst in its path.
Four more people died in Mozambique, local authorities said, as an assessment of the damages was underway after the record-breaking storm made its second landfall in the country on Saturday.
Mozambique's public broadcaster TVM reported that one person was killed near the port of Quelimane when their house collapsed, bringing the number killed to at least 28 in Mozambique and Madagascar since Freddy first made landfall last month.
The full extent of the damage and loss of life in Mozambique is not yet clear, as the power supply and phone signals were cut off in the affected area.
Scientists say climate change is making tropical storms stronger, as oceans absorb much of the heat from greenhouse gas emissions and when warm seawater evaporates heat energy is transferred to the atmosphere.
This report was produced with data from Reuters and Agence France-Presse.