Mohammed Adow, reporting for Al Jazeera from flood-hit Soroti in northern Uganda, said that roads "which would have been the way to bring in the food aid and the medicine have been swept away and destroyed in many places.
"Farmers we have spoken to have said their crops have been destroyed.
"We've seen houses that have been destroyed, with their owners now living in primary schools - sleeping the in the schools during the night and leaving in the morning when the children come in for their lessons."
In eastern Uganda, nine people have been reported killed and 150,000 made homeless since early August.
Another 400,000 people, mainly subsistence farmers, have lost their livelihoods after their fields were flooded or roads washed away.
The rains are forecast to worsen in the next month.
As the rains continue, WFP in Uganda said it is also bracing for an influx of thousands fleeing fighting in eastern Congo.
On the night of August 30, some 30,000 asylum seekers entered Uganda, the group said, though most have returned home.
On the other side of the continent, Ghana in west Africa has also been heavily hit.
Three regions in the country's north have been declared an official disaster zone after whole towns and villages were submerged.
Torrential rains between July and August killed at least 18 people and displaced a quarter of a million, Oboshie-Sai Cofie, Ghana's information minister, said over the weekend.