Five homes were also swept away by floodwater. Maputo mayor, David Simango, visited the affected neighbourhoods.
People living in flood-prone areas of the coastal city would be moved to safe zones, according to the city's health and social welfare councillor, Nurbai Calu.
"For those families who have lost their houses, in the first place we want to guarantee that they are in good health and have a roof over their heads," said Calu, according to the Mozambican news agency, AIM. "We have nobody sleeping in the open."
In the neighbouring city of Matola, about 300 people were left homeless after 19 houses collapsed and another 370 were flooded, reported the news agency. Hundreds of people have also been displaced in the southern city of Xai Xai.
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Mudslides have damaged roads, making it difficult to reach affected areas. The water was waist-high as people were forced to evacuate their homes, carrying as many of their belongings as they could.
In October this year, the Mozambican government announced that it had set aside $32 million of its national budget to deal with flooding and avoid possible disaster.
Last year, flooding in the north and central parts of the country killed at least 55 people and displaced nearly 170,000 people.