Cyclone Freddy, packing powerful winds and torrential rain, killed at least 70 people in Malawi and Mozambique on its return to southern Africa's mainland, authorities said Monday.

Freddy, on track, to become the longest-lasting storm on record, barrelled through southern Africa at the weekend for the second time within a few weeks, making a comeback after a first hit in late February.

More than 60 bodies were found during the day in southern Malawi where heavy downpours triggered flooding, according to the Red Cross.

"Sixty-six people have died in Malawi, 93 injured and 16 people are missing due to Tropical Cyclone Freddy," tweeted the humanitarian organisation, which is helping with search and rescue operations.

President Lazarus Chakwera declared a "state of disaster in the Southern region" of the country after he "noted with grave concern the devastation that Cyclone Freddy is currently bringing".

The government in one of the poorest countries in the world is already responding to the disaster while appealing for local and international relief aid for the affected families, it said.

At least 36 bodies were found in one township of Chilobwe, in Blantyre, a vast city of more than one million people, regional police spokeswoman Beatrice Mikuwa said, adding the township was "hit the most", with dozens of houses washed away.

Incessant rains were hampering rescue efforts, said Mikuwa.

Richard Duwa, 38, said his sister-in-law's family was swept away by flash floods.

"We got a call from the neighbours at around five am to say that 'your relations have been washed away by the rains'," Duwa, a government clerk, told AFP.

At least four other people died in neighbouring Mozambique, local authorities said.

The Mozambique National Institute for Disaster Management (INGD)  was still assessing, but said the fallout from the storm's second landfall in the country was worse than expected.

"The number of affected people was above the forecast," INGD head Luisa Meque said, adding the storm struck also areas that had been "deemed safe".

Malawi has ordered schools in ten southern districts to remain closed until Wednesday, with rains and winds expected to continue to batter the nation's south.

National carrier Malawi Airlines said all flights to Blantyre have been cancelled until further notice after an inbound plane ran into the bad weather mid-flight and was forced back to the capital Lilongwe.