"There is no way Malawi can cope with it's own resources," said Lucius Chikuni. "The president is expected to declare a disaster and make a formal appeal for international assistance today."
Early assessments show that up to 15,000 families - with an average of five members each - have been affected with at least a quarter losing their homes.
Affected areas include Phalombe, Mwanza, Ntcheu, Balaka and Salima districts in the centre and south of the country.
Chikuni's office would help the victims with food items, plastic sheeting, basic household items like pails, plates, cups, pots and blankets and have supplied a few family-size tents. Many people were taking shelter in churches and schools.
About 14 small bridges were washed away and a number of railway bridges have been closed. The government has carried out the temporary rehabilitation of the road link between Lilongwe and Blantyre.
Health officials were also addressing the threat of a cholera outbreak in the Salima district.
"Weather forecasters say we should expect worse conditions over the next few days," said Chikuni, whose own home sustained damage.
The World Food Programme (WFP) said the heavy rains had cut off up to 10 percent of its beneficiaries from deliveries.
"We have been told that 4,000 ha of crops have been destroyed in Salima alone and that 906 houses were destroyed in the Dzaleka refugee camp in Dowa," WFP spokeswoman Jennifer Abrahamson told IRIN.
The Lilongwe/Nacala rail link, a route used to transport food aid from the Mozambican port, was cut when a locomotive and 11 carriages derailed, she said.
"This is a great concern to us because it poses a problem with food delivery [from the port to Malawi] at this crucial time," Abrahamson said.
WFP plans to supply relief food to 2.8 million people throughout the country in January.
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