"The situation is very dire," said Guilherme Botelho, emergency project coordinator for Doctors Without Borders (MSF) in Malawi.
"There are many casualties, either wounded, missing or dead, and the numbers will only increase in the coming days," he said.
Many people perished in mudslides that washed away homes in the country's commercial capital, Blantyre.
Across the country, nearly 59,000 people have been affected and more than 19,000 displaced, with many now sheltering in schools and churches.
Freddy was still causing localised rains and winds in southern Malawi on Tuesday, but conditions were expected to ease from Wednesday evening, according to the country's meteorological service.
'We feel helpless'
In Chilobwe, a township outside Blantyre, stunned survivors surveyed flattened houses and other structures as rain continued to fall.
John Witman, in his 80s, dressed in a raincoat and woollen hat with his 10 family members in tow, stood in front of what had been his son-in-law's home. It was now just rocks and gushing water, the house having been swept away.
"I wish that we could find him, and find closure. We feel helpless because no one is here to help us," he said.
In Chimwankhunda, a few kilometres away, Steve Panganani Matera, wearing a high-visibility green jacket, pointed to a mound of mud.
"There were plenty of houses, but they are all gone," Matera said. "There are plenty of bodies down there in the mud."
Fourteen-year-old Mayeso Chinthenga said his family's house was taken by the cascading mud.
"We were out looking for firewood when we saw rocks rolling down the mountain so we ran for safety. Some of our neighbours died on the spot," he said at a nearby school.
President Lazarus Chakwera, who returned to the country on Tuesday after attending a United Nations conference in Qatar, hailed the relief efforts by volunteers.
"We have arrived to a devastated nation," he said in a statement.
Cyclone Freddy reached landlocked Malawi early on Monday morning after sweeping through Mozambique at the weekend.
The storm has unofficially broke the World Meteorological Organization's benchmark as the longest-lasting tropical cyclone on record, set in 1994 for a 31-day storm named John.
Freddy became a named storm on February 6, making landfall in Madagascar on February 21 and sweeping over the island before reaching Mozambique on February 24, claiming nearly two dozen lives in both countries and affecting nearly 400,000 people.
It then returned to the Indian Ocean and gathered new energy over its warm waters, then reversed course to come back much more powerful at the weekend, packing wind gusts of up to 200 km/h (125 mph), according to Emmanuel Cloppet of the Meteo-France weather service.
Meteorologists say that cyclones tracking across the entire Indian Ocean are very infrequent -- the last occurred in 2000 -- and that Freddy's loopback was even more exceptional.
"It's a very rare thing that these cyclones feed themselves over and over again," said climate expert Coleen Vogel at South Africa's University of the Witwatersrand.
The cyclone has piled more woes on Malawi, already grappling with the deadliest cholera outbreak in its history, which has killed over 1,600 people since last year.
Fears of a cholera resurgence after the outbreak started in the aftermath of another tropical storm last year have been exacerbated by vaccines shortages.