"We are asking people to move to safer areas. We estimate there are 55 000 people affected," a spokesperson for Mozambique's Disaster Relief Management Institute, Rita Almeida, told the media on Tuesday.
Emergency teams are already in place and motorboats have been dispatched to the area to take people to safe ground.
The south and the centre of the country have been placed on red alert after experiencing the heaviest rainfalls seen since devastating floods killed around 800 people in 2000.
The latest downpours have already killed 35 people since the start of the rainy season in October, and eight major rivers are above crisis levels.
Experts predict that the southern town of Chokwe – which saw water rise to roof level in previous floods – could again bear the brunt of the floods.
"The situation is critical," said Elidio Jamisse, a United Nations Development Programme advisor to Mozambique's emergency response service.
"The Massingir Dam on the Elephant River [a tributary of the Limpopo] is already at 3 500 cubic metres per second," he said, noting: "This water will join the water from the Limpopo. All this water is headed for Chokwe."
Areas to the north of the town, where the river had risen to more than 11 metres, were already under water.
"When these 11.8 metres of water arrive in Chokwe, it will be added to the water that is already above the level of alert," Jamisse said.
"The prediction is that starting tomorrow it will arrive in Chokwe. That is why all our teams are working to evacuate people."
From Sunday to Monday almost 185 millimetres of rain poured over the Limpopo River basin in southern Gaza province, where the most vulnerable communities live.
Preparing for the worst-case scenario
Figures from the Mozambican National Water Directorate on Tuesday showed that the south-eastern town of Panda received some 233 millimetres of rain between Monday and Tuesday.
International organisations are preparing for the worst-case scenario.
"There is a big dyke in Chokwe that is giving problems. They are afraid if that dyke breaks, all those people will have to move rapidly," World Food Programme country head Lola Castro said.
The evacuees will be housed in 10 temporary accommodation centres, she said.
Rains in neighbouring countries also swelled rivers, and authorities opened the sluices from two dams in the south to lower dangerous levels.
Coastal Mozambique is home to nine international river basins, making it especially vulnerable to flooding.
Effects on neighbouring countries
Although the rainfall has stopped in most areas, the risk of flooding remains high as waters arrive from further inland.
Neighbouring South Africa has been hit by torrential rains, and the Limpopo River, which flows to Mozambique's Xai-Xai in the affected Gaza province, has flooded.
Authorities in South Africa's giant wildlife reserve Kruger National Park, which borders Mozambique, were also forced to evacuate dozens of tourists and staff.
At least eight people have died in the northern-most district of Vhembe in Limpopo province. – Sapa-AFP