"We already have more than 200 dead, and nearly 350,000 people are at risk," Mozambican President Filipe Nyusi announced Tuesday, while the government in Zimbabwe said around 100 people had died but the toll could be three times that figure.
The UN, meanwhile, said that one of the worst storms to hit southern Africa in decades had also unleashed a humanitarian crisis in Malawi, affecting nearly a million people and forcing more than 80,000 from their homes.
The city of Beira in central Mozambique bore Cyclone Idai's full wrath on Thursday before the storm barrelled on to neighbouring Zimbabwe, unleashing fierce winds and flash floods and washing away roads and houses.
Ninety percent of the city of some 530,000 people and its surrounding area has been "damaged or destroyed," it said in a statement.
"Almost everything is destroyed. Communication lines have been completely cut and roads have been destroyed. Some affected communities are not accessible," IFRC's Jamie LeSueur said.
A large dam burst on Sunday and cut off the last road to Beira, he said.
Emma Beaty, coordinator of a grouping of NGOs known as Cosaco, said: "We've never had something of this magnitude before in Mozambique".
"Some dams have broken, and others have reached full capacity, they'll very soon open the flood gates. It's a convergence of flooding, cyclones, dams breaking and making a potential wave: everything's in place so we get a perfect storm."
Beira international airport was closed because of cyclone damage but later reopened.
Neighbouring Zimbabwe hit
In neighbouring Zimbabwe, Idai has left over 80 dead and at least 150 more missing, according to the Zimbabwe Red Cross.
The eastern district of Chimanimani was worst-hit, with houses and most of the region's bridges washed away by flash floods.
The most affected areas are not yet accessible, and high winds and dense clouds have hampered military rescue helicopter flights.
"We have 200 volunteers searching for the missing and distributing food to displaced people," said Karikoga Kutadzaushe, Operations Manager, Zimbabwe Red Cross Society.
Two pupils and a worker at a secondary school in the area were among those killed after a landslide sent a boulder crashing into their dormitory.
Soldiers on Sunday helped rescue the surviving nearly 200 pupils, teachers and staff who had been trapped at the school in Chimanimani.
Joshua Sacco, lawmaker for Chimanimani, told AFP that between "150 to 200 people" are missing.
The majority of them are thought to be government workers, whose housing complex was completely engulfed by raging waters. Their fate was unknown because the area was still unreachable.
Zimbabwean President Emmerson Mnangagwa cut short a visit to Abu Dhabi, saying on his return home on Monday, "we are deeply grieved as a nation".
His government has come under fire for failing to evacuate people in time.
Misery in Malawi
The number of people killed in floods in southern Malawi is "close to 60," according to the homeland security minister, Nicolas Dausi who added that "700,000 thousand people have been affected by Idai."
Almost 83,000 people have been displaced by since storms that began more than a week ago caused rivers to break their banks, leaving villages underwater, and knocked out power and water supplies in some areas.
An early warning system managed by South Africa was triggered days before Idai made landfall. Authorities in all of the affected countries received information about the impending storm.
"The early warning system did its job, but people were slow to respond to the early warning systems because it had already been raining for several days," Dausi explained.
Meanwhile thousands of families are sheltering in churches, village halls and schools. The race is on to feed the displaced in the short term. In the medium term many of these people are likely to depend on food aid for several months to come due to crop damage caused by cyclone Idai.