The death toll from Cyclone Freddy in Malawi is slated to surpass 1,200 after authorities said Thursday hundreds of missing people would be declared dead as hopes of finding survivors fade.

Freddy dumped six months' worth of rainfall on southern Malawi in six days earlier this month, triggering floods and mudslides that swept away homes, roads and bridges in a record-breaking deluge.

At least 676 people died and 538 are still missing, according to authorities.

On Thursday police said those missing would be presumed dead upon completion of rescue operations, which were still ongoing in some areas.

"We are still reaching out to some places that were previously inaccessible," police spokesman Harry Namwaza told AFP.

"When we are done with the process, then it will be the appropriate time for us to declare that the missing are presumed dead."

The department of Disaster Management Affairs has said rescue efforts are scaling back.

"Looking at the number of days that have gone by, the possibilities of finding anyone alive are slim," disaster management commissioner Charles Kalemba said on Wednesday.

Sniffer dogs in the hard-hit city of Blantyre have been decommissioned, as crews on the ground felt they "had done the best that they could", he said.

Cyclone Freddy first struck southern Africa in late February, hitting Madagascar and Mozambique, leaving Malawi unscathed.

The storm then moved back out over the Indian Ocean, where it drew more power from the warm waters before making a rare course reversal to slam into the mainland a second time.

The overall toll of the cyclone across all the countries impacted could reach almost 1,400 if all of Malawi's missing are to be declared dead.

The storm killed 165 people in Mozambique and 17 in Madagascar, according to the United Nations.