A state of emergency has been declared in 15 of Malawi’s 28 districts, and 63,000 hectares of land are under water, the Food and Agriculture Organisation (FAO) reported.
(READ MORE: Malawi says to miss 2015 economic growth forecast after deadly floods)
In one district alone, 153 people are still missing, the FAO said, and the death toll is expected to rise.
"Displaced people are either in camps or hosted by relatives," Florence Rolle, a senior FAO official in Malawi told the Thomson Reuters Foundation.
One of the world's poorest and most densely populated countries, about 85 percent of Malawi's population of 17.5 million are farmers living in rural areas.
"Some of the affected people have lost everything: their crops, livestock, homes and seeds," Rolle said.
"There is (a) narrow window of opportunity for farmers to replant if a food crisis is to be averted later in the year," she said.
The government has committed $16 million (10.55 million pounds) for the agricultural sector to help affected farmers buy seeds and other necessities.
Heavy rains began in Malawi earlier this month, leading rivers to burst their banks and creating flash floods.
(WATCH VIDEO: Impact of floods in Malawi)
In some villages, only the tops of banana trees can be seen emerging from the floodwaters.
Flooding is not uncommon in the landlocked country, but the scale of this year's devastation is unprecedented, Rolle said.
Climate change, deforestation and rapid population growth are exacerbating the effects of the rainy season, making the current floods some of the worst in 30 years, she added.