Government and aid agency officials sounded the alarm on Tuesday after flights over a vast area of wreckage wrought by Cyclone Idai in Zimbabwe, Malawi and especially Mozambique spurred fears of a massive human toll.

That toll is already in the hundreds across the three southeast African countries. Mozambique's president told state radio Monday that deaths in his country could surpass 1,000.

A family dig for their son who got buried in the mud when Cyclone Idai struck in Chimanimani. Photo / AP
A family dig for their son who got buried in the mud when Cyclone Idai struck in Chimanimani. Photo / AP

Aerial footage showed miles and miles of submerged areas, both rural and urban. Mozambique's fourth-largest city, Beira, appeared worst hit, with the Red Cross estimating that 90 per cent of the buildings in the city of half a million people were damaged or destroyed. The storm made landfall with sustained winds equivalent to a Category 2 hurricane in a region with weak infrastructure.

An aerial view of the destruction of homes after Tropical Cyclone Idai, in Beira, Mozambique. Photo / AP
An aerial view of the destruction of homes after Tropical Cyclone Idai, in Beira, Mozambique. Photo / AP

One of the few areas in Beira that remain above the floodwaters, the city's airport, became a staging ground for humanitarian relief efforts. On flights over the city and surrounding areas, aid workers said, they saw hundreds of people crammed onto rooftops, in the branches of palm trees and on small hillocks, waiting to be rescued.

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Flood waters cover large tracts of land in Nicoadala, Zambezia Province of Mozambique. Photo / AP
Flood waters cover large tracts of land in Nicoadala, Zambezia Province of Mozambique. Photo / AP

Heavy rains are expected to continue through Tuesday. The United Nations estimated that more than 2.5 million people need immediate assistance. And with the crops and homes of thousands of families destroyed, a prolonged humanitarian crisis appeared inevitable.

People salvaging what is left of their belongings after Tropical Cyclone Idai, in Beira, Mozambique. Photo / AP
People salvaging what is left of their belongings after Tropical Cyclone Idai, in Beira, Mozambique. Photo / AP

"There's a sense from people on the ground that the world still really hasn't caught on to how severe this disaster is," Matthew Cochrane, a spokesman for International Federation of Red Cross and Red Crescent Societies, told a UN briefing in Geneva.

Heavy rains fell in the region ahead of the cyclone's landfall, paving the way for an unprecedented storm surge and the breaching of rivers. More than 120 people were killed by the earlier rains in Malawi, where drought conditions gave way to flooding. Malawi's government has reported 56 additional deaths since Idai made landfall.

People walk through debris on the streets of the city of Beira, Sofala Province, Mozambique, after Cyclone Idai made land fall. Photo / AP
People walk through debris on the streets of the city of Beira, Sofala Province, Mozambique, after Cyclone Idai made land fall. Photo / AP

Beira lies at the mouth of a large estuary. The city is home to a major port that is essential for the supply of gas and food to the central part of the country, as well as to Zimbabwe and Malawi, which are landlocked. The paralyzation of Beira has raised fears of imminent goods shortages across the region.