More than 238 were dead, hundreds were missing and thousands more were at risk.
"This is the worst humanitarian crisis in Mozambique's recent history," said Jamie LeSueur, head of response efforts in Beira for the International Federation of Red Cross and Red Crescent Societies. At least 400,000 people have been left homeless.
The rapidly rising floodwaters created "an inland ocean" in Mozambique, endangering tens of thousands of families, aid workers said as they scrambled to rescue survivors of Cyclone Idai on Tuesday and airdrop food, water and blankets.
Mozambique's President Filipe Nyusi said the death toll could reach 1000.
Emergency workers called it the region's most destructive flooding in 20 years. Heavy rains were expected to continue through Thursday.
"This is a major humanitarian emergency that is getting bigger by the hour," said Herve Verhoosel of the World Food Programme. Many people were "crammed on rooftops and elevated patches of land outside the port city of Beira" and WFP was rushing to rescue as many as possible, he said.
Mozambique's Pungue and Buzi rivers overflowed, creating "inland oceans extending for miles and miles in all directions," Verhoosel said. Dams were at 95% to 100% capacity.
"People visible from the air may be the lucky ones and the top priority now is to rescue as many as possible," he said.
The extent of the damage was not yet known as many areas remained impassible. With key roads washed away, aid groups were trying to get badly needed food, medicine and fuel into hard-hit Beira, a city of some 500,000 people, by air and sea.
Cyclone Idai swept across central Mozambique before dropping huge amounts of rain in neighboring Zimbabwe's eastern mountains. That rainfall is now rushing back through Mozambique, further inundating the already flooded countryside.
"It's dire," Caroline Haga of the Red Cross told The Associated Press from Beira. "We did an aerial surveillance yesterday and saw people on rooftops and in tree branches. The waters are still rising and we are desperately trying to save as many as possible."
Satellite images were helping the rescue teams target the most critical areas, Haga said. Rescue operations were based at Beira airport, one of the few places in the city with working communications.
The waters flooded a swathe of land more than 48km in central Mozambique putting more than 100,000 people at risk, said the aid group Save the Children.
"The assessment emerging from Mozambique today is chilling," said Machiel Pouw, Save the Children's response leader in Mozambique. "Thousands of children lived in areas completely engulfed by water. In many places, no roofs or tree tops are even visible above the floods."
"The full horror, the full impact is only going to emerge over coming days," Red Cross spokesman Matthew Cochrane told reporters in Geneva.
Torrential rain was still lashing the region on Tuesday, and Buzi town could be entirely submerged within 24 hours, the aid group said.
Hardest hit was Beira, where thousands of homes were destroyed.
The city and surrounding areas were without power and nearly all communication lines were destroyed. Beira's main hospital was also badly damaged. Large areas to the west of Beira have been severely flooded and flood waters have completely covered homes, telephone poles and trees, the Red Cross said.
Beira could face a "serious fuel shortage" in the coming days, WFP said, and its power grid was expected to be non-functional through the end of the month.
In Zimbabwe the death toll rose to 98, the government said. The mountain town of Chimanimani was badly hit. Several roads leading into the town were cut off, with the only access by helicopter. Residents expected the death toll to rise.
"We did over 38 burials this morning," Absolom Makanga, a Salvation Army divisional commander, told the AP. "It is difficult. We have to walk long distances because the roads are cut off but also because sometimes the graves are then washed away."
Among those fleeing on foot was Luckmore Rusero, who carried a small bag with his remaining possessions. His wife carried their 1-year-old child while their 11-year-old son struggled to keep pace as they joined many others in seeking refuge.
"Thank God we survived. There are no roads, no transport, so we have been walking for more than 20 kilometers now through the forests and the mountains," Rusero said.
Some escaped with nothing but their lives.
"I fled naked," Tecla Chagwiza said. "I only received clothes in the morning from well-wishers who are also helping me with food." She said her family's home was destroyed and three neighbors were dead. Others were missing.
Zimbabwean President Emmerson Mnangagwa arrived in the area on Tuesday, saying a number of countries, including the United Arab Emirates, South Africa, Botswana, Namibia and Angola, were offering aid.
The United States Embassy in Zimbabwe said the US was also "mobilising to provide support" to partners in the three affected countries, but provided no details. The European Union and Britain also pledged aid.
Malawi's government confirmed 56 deaths, three missing and 577 injured in the flooding, which caused rivers to burst their banks, leaving many houses submerged and around 11,000 households displaced in the southern district of Nsanje.
Neighbouring Tanzania's military airlifted some 238 tons of emergency food and medicine to the three countries.
