Mozambique's army has been ordered to evict some 2,500 people who refuse to leave their homes despite the floods.
Mozambique was not prepared for the floods in 2000 and 2001
Prime Minister Luisa Diogo said the floods could be worse than those of 2000 and 2001 but she said the country was now better prepared.
"The possibility of an emergency is still there," she said.
Strong winds, heavy rains and flooding have so far claimed at least 29 lives, destroyed more than 4,600 houses, 100 classrooms and four health centres.
Some 700 people died in devastating floods in Mozambique in 2000 and 2001.
The BBC's Jose Tembe in the capital, Maputo, says people want to stay to protect their homes, crops and animals.
Some feel that the flooding is not yet serious enough to warrant moving, he says.
But Ms Diogo said the situation was likely to get worse.
"The possibility of an emergency is still there. But the government is prepared to face the situation," she told the Reuters news agency.
The situation is worst in the country's central region where the Zambezi River and its tributaries - the Shire and Revubue - have become swollen with surging waters from neighbouring Malawi, Zambia and Zimbabwe.
Mozambique's National Disasters Management Institute director Paulo Zucula says some 46,500 people could be affected.
Some are already living in temporary accommodation centres.
Rescue operations are due to start in the Zambezi Valley next Tuesday.
The relief agency has set up an operations centre in the central town of Caia and has boats and helicopters on hand to rescue anyone trapped by the rising waters.
Assistance is also available from naval units of the Mozambican armed forces.
The agency had made contingency plans for dealing with serious flooding this rainy season, and had put aside tents, blankets, chlorine for purifying drinking water, and other relief goods at key positions.
But these are only enough until the end of this month, our reporter says.
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