Mr Nyusi flew over areas that were otherwise accessible, some of which had been hit by flooding before Cyclone Idai.
In Beira, Mozambique’s fourth-largest city and home to 500,000 people, a large dam had burst, further complicating rescue efforts.
Large swathes of land were completely submerged, and in some streets people waded through knee-high water around piles of mangled metal and other debris.
In the early hours of Monday morning, rescuers launched dinghies onto chest-high waters, navigating through reeds and trees — where some people perched on branches to escape the water — to rescue those trapped by the flooding.
Meanwhile, rescuers were struggling to reach people in Zimbabwe’s Chimanimani district, cut off from the rest of the country by torrential rains and winds of up to 170 km per hour that swept away roads, homes and bridges and knocked out power and communication lines.
Zimbabwean information ministry official Nick Mangwana told Reuters the number of confirmed deaths throughout the country was now 89. The body count is expected to rise.
Many people had been sleeping in the mountains since Friday, after their homes were flattened by rock falls and mudslides or washed away by torrential rains.
The Harare government has declared a state of disaster in areas affected by the storm. Zimbabwe, a country of 15 million people, was already suffering a severe drought that has wilted crops.