Freddy is one of the strongest storms ever recorded in the southern hemisphere and could be the longest-lasting tropical cyclone, according to the World Meteorological Organisation.

It pummelled central Mozambique on Saturday, ripping roofs off buildings and bringing widespread flooding around the port of Quelimane before moving inland towards Malawi with torrential rains that caused landslides.

The full extent of the damage and loss of life in Mozambique in particular is not yet clear, as the power supply and phone signals were cut off in some parts of the affected area.

The storm has killed 99 people in Malawi, including 85 in the main commercial hub of Blantyre, the commissioner of the Department of Disaster Management Affairs Charles Kalemba said at a press briefing.

The total number killed by storm Freddy in Mozambique, Malawi and Madagascar since it first made landfall last month is now about 135.

The central hospital in Blantyre had received at least 60 bodies by early afternoon, Doctors Without Borders (MSF) country director Marion Pechayre told Reuters by telephone, adding that 200 injured were being treated in the hospital.

The injuries were from falling trees, landslides and flash floods, she said.

"A lot of (houses) are mud houses with tin roofs, so the roofs fall on people's heads."

Police spokesman Peter Kalaya told Reuters that rescue teams had been looking for people in Chilobwe and Ndirande, two of the worst-affected townships in Blantyre, the country's second-largest city, where it was still raining on Monday and many residents were without power.

"Some missing people are feared buried in rubble," Kalaya said.

Malawi's electricity company EGENCO said that power generation capacity was unstable and that it had experienced total system shutdown twice on Monday.

It has shut down all major hydro power stations to protect them from damage, it said.

At least ten people died in Mozambique's Zambezia province, a provincial delegate from the National Institute of Disaster Risk Management, Nelson Ludovico, said on public broadcaster Radio Mozambique, adding that the figures were still provisional.

"The situation is critical in Zambezia province. We can't advance with an accurate picture of the scale of damage because there's no communications with all the regions," Health Minister Armindo Tiago said on public radio.

Guy Taylor, chief of advocacy for United Nations children's agency UNICEF in Mozambique, told Reuters from Quelimane that humanitarian agencies there did not have the capacity to deal with a disaster of this size.

"We saw a lot of destroyed buildings and clinics. People's homes had their roofs torn off by the wind. Even before the cyclone hit we saw localised flooding," he said.

The wind had died down on Monday but there was still a lot of flooding that had destroyed crops and created a risk of waterborne diseases, he said.

Mozambique has had more than a year's worth of rainfall in the past four weeks.

Australian Associated Press