"What the country has witnessed is only the beginning of the onset of rains," Paul Chiunguzeni, principal secretary for Disaster Management Affairs, said in a statement.
"The government is urging people living in flood-prone districts to urgently relocate to upland areas to avoid losing more lives."
The floods, which have wreaked havoc on half the country's 28 districts, have left an estimated 100,000 homeless.
Government on Tuesday put the death toll at 48, though Chiunguzeni would not provide an updated figure, saying teams had been sent to "source and verify information" on the number of people dead and missing.
And the rains are expected to continue.
Hein Zeelie of the UN Office for the Coordination of Humanitarian Affairs (OCHA) said the central and northern parts of the country were the agency's next concern "as we are expecting heavy rains for those areas for the next week".
"A lot of preparation activities have been taking place for the rainy season, but no matter how well prepared one could have been, the extreme amount of rainfall would have led to this situation."
The country's sole electricity provider Escom lost 35 percent of its power after shutting down two of its five power stations located on Shire River.
This was after the floods left a "high volume of trash, silt and huge logs which have choked the water entry points of the machines," causing massive power outages across Malawi, according to Escom CEO John Kandulu.
Government has also warned of the impact the floods will have on health services, fearing the spread of water-borne diseases.
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