The president has declared a third of the country a disaster zone and urgently appealed for foreign aid.
Reports from neighboring Mozambique said a group of 25 schoolchildren were swept away by floodwater on January 12.
Heavy regional rain began last month and forecasters say they expect it to continue over the coming days.
Peter Mutharika said his government alone did not have the money to cope.
Homes and crops in Malawi were destroyed by the rising torrents while roads and railways have also been cut off.
One government official said many victims died when villages were flooded in Mangoche district, an area in the south about 60 miles south of Blantyre, the commercial capital.
“People have fled into schools and churches on higher ground, others are in the open because there is not enough space,” said Grey Mkwanda, a district planning officer, speaking to the Associated Press news agency.
He added that some victims in Blantyre had perished when their homes collapsed.
According to the city’s police spokesman, Elizabeth Divala, search teams are still looking for two children who went missing during the floods.
The rising waters have been caused by late summer storms in the region.
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