An aerial survey of Mozambique's cyclone-hit province shows that a 50km (30 mile) stretch of land is under water, charity Save The Children says.
The flooding was caused after River Buzi burst its banks, it adds.
President Filipe Nyusi said at least 1,000 people could have been killed by Cyclone Idai which made landfall near the port city of Beira on Thursday with winds of up to 177 km/h (106 mph).
Neighbouring Zimbabwe and Malawi have also felt the impact.
Mozambique's government says 600,000 people have been affected and 100,000 need to be urgently rescued near Beira.
Buzi town, which is estimated to be home to more than 2,500 children, could be under water within 24 hours, Save The Children warned.
In Zimbabwe, the government says 98 people have been killed and more than 200 are missing.
President Emmerson Mnangagwa said that the government was conducting rescue missions and delivering food aid.
The UN says the storm is possibly the worst weather-related disaster ever to hit the southern hemisphere, the Reuters news agency reports.
Floods of up to six metres deep had caused "incredible devastation" over a huge area, World Food Programme regional chief Lola Castro said.
At least 1.7 million people were in the direct path of the cyclone in Mozambique and 920,000 have been affected in Malawi, the UN said.
In Zimbabwe, at least 20,000 houses have been partially damaged in the south-eastern town of Chipinge, 600 others were completely destroyed.
Local officials say they are distributing rice and maize from the national food reserve to those displaced.
In Mozambique, several aid agencies are assisting government efforts in the search and rescue operations and in the distribution of food aid, ReliefWeb reports.
Telecoms Sans Frontiers has sent a team to Beira to help set up communication networks - which has been severely hindered - for humanitarian operations.
Many aid trucks are stuck on the impassable roads and unable to reach their destinations. The conditions have also limited air operations.
The WFP team on the ground is assisting nearly 900 families affected by flooding with a mixture of cash transfer and vouchers.
Mozambique's National Institute for Disaster Management is also housing 3,800 families in Sofala province.
A cargo plane carrying emergency supplies is also expected to arrive in Mozambique on Tuesday, Sacha Myers, from Save The Children, told the BBC.