Cyclone Idai hit Mozambique's port city of Beira with winds of up to 170 kph last Thursday, then moved inland to Zimbabwe and Malawi, flattening buildings and putting the lives of millions at risk.

At least 200 people have died in Mozambique and 98 in Zimbabwe, but the death toll is likely to rise as rescuers are still finding bodies.

Hundreds were clinging onto trees or roofs on Wednesday, waiting for rescue teams. Roads in and around Beira were swamped and heavy rain was continuing to fall, complicating rescue efforts and meaning that aid had to be flown in by helicopter or plane.

The floods have also brought the threat of waterborne diseases.

"The first thing you see when you arrive is destruction, and a lot of water," Get Verdonck, an emergency coordinator with the aid group Doctors Without Borders, said from Beira.

"People are using well water with no chlorination, and that water is unlikely to be clean, ... pneumonia and other respiratory diseases are going to be a problem."

Mozambican President Filipe Nyusi has declared three days of national mourning and has said the eventual death toll from the cyclone and ensuing floods could rise to more than 1,000.

In the eastern Zimbabwe, grieving families rushed to bury their dead because the cyclone had knocked out power supplies and put mortuaries out of action.

Zimbabwean President Emmerson Mnangagwa said on a visit to the town of Chimanimani that his government would ensure houses were built with stronger materials in future.

Malawi has not released details of casualties from the storm, which weakened as it moved further inland. More than 50 people had already died in floods the week before the cyclone hit.

Drone footage showed residents of a shantytown in Beira still picking through wreckage almost a week after the storm hit and trying to drag plastic sheeting over their ruined homes.

The UN children's fund, UNICEF, estimated that 260,000 children were at risk from the devastation in the area.

Beira, a low-lying city of 500,000 people, is home to Mozambique's second-largest port and serves as a gateway to landlocked countries in the region.

The European Union said it will provide initial emergency aid of 3.5 million euros ($A5.6 million) to Mozambique, Malawi and Zimbabwe for emergency shelters, hygiene, sanitation and healthcare. Britain and the United Arab Emirates have also pledged aid.

"Great floods have sowed mourning and devastation in various areas of Mozambique, Zimbabwe and Malawi," Pope Francis said on Wednesday.

"I express my pain and closeness to those dear people."

Australian Associated Press