Cyclone Jokwe, which made landfall on Saturday, has also destroyed thousands of dwellings, hundreds of schools and dozens of hospitals, the Institute for the Management of National Disasters said on Monday.
Paulo Zucula, the Institute's director, said Cyclone Jokwe was more dangerous than Cyclone Favio, which struck Mozambique last year.
Zucula said more floods could be expected as the cyclone is expected to move inland to areas in central Zambezia province already hit by floods earlier this year.
The cyclone was expected to lose intensity from Tuesday onwards, according to the national institute of meteorology (NIM).
Authorities in these regions have issued a red alert and invited people living in makeshift shelters to take refuge in public buildings.
Mozambique has been battling floods since January that have killed about 10 people and displaced another 100,000.
The rising waters destroyed more than 80,000 hectares of farmland, leaving some 250,000 people dependent on international food aid.