Cyclone Jude hit the Indian Ocean country on Monday, bringing winds of up to 195 kilometres (more than 120 miles) an hour and more than 250mm (10 inches) of rain over 24 hours, the National Institute of Meteorology said.
It is the third cyclone to strike impoverished Mozambique in four months.
At least six people were killed and 20 hurt in the storm, the National Institute for Risk and Disaster Management said in a statement. More than 900 houses were destroyed and 9,500 people affected, it said.
Jude weakened to a tropical storm but continued to bring intense rain, strong winds and thunderstorms, it said.
Cyclone Chido struck the Portuguese-speaking country in December, causing the deaths of at least 120 people and destroying almost 120,000 homes, according to official data.
In mid-January, Cyclone Dikeledi caused the deaths of at least five people and destroyed nearly 3,500 homes.
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