"The impact of the floods on food production is a real threat to the country and could lead to a major food crisis," said Hussaini Abdu, Nigeria director of the CARE charity.
"Flooding is still ongoing but we can safely say that between 60 to 75 percent of the yield we expected is going to be lost," Kabir Ibrahim, president of All Farmers Association of Nigeria, told AFP this week.
Nearly 110,000 hectares of farmland have been completely destroyed by flooding since August according to the latest government figures.
Officials and residents blame climate change but also poor planning and the release of excessive water from dams, a process that is meant to ease pressure.
"If you don't open the water through the spillways, then dams will break," said Ibrahim, and then "it would be like Pakistan. All of Nigeria would be under water like Pakistan."
Ibrahim, whose organization represents 20 million farmers, believes "there will be more hardship towards the end of the year and beginning of next year."
The floods have not just destroyed farmlands, they have also prevented the transport of trucks and damaged roads and bridges, further pressuring the food supply.
"We were hoping inflation would get a break with the (upcoming) harvest but now with the floods, it puts a big question mark on our forecast on inflation," said Ari Aisen, the IMF's Resident Representative for Nigeria.
The flooding has worsened a situation already hit by supply shortages.
Food inflation year-on-year was already at 23.3 percent last month, in part because of ripple effects on the import-dependent country from the coronavirus pandemic and the Russia-Ukraine war.
The World Food Program and the UN's Food and Agriculture Organization (FAO) said last month that Nigeria was among six countries facing a high risk of catastrophic levels of hunger, even before the floods.
While immediate assistance is now needed, the International Monetary Fund said it would be less costly to invest in preventive measures and policies.
Countries should invest to "help populations adapt to these types (of) events rather than using resources after the fact," said Aisen.
But in the meantime, the government said it was ramping up support to affected communities.
President Muhammadu Buhari approved the release of 12,000 metric tons of assorted grains from a national strategic reserve stock.
But farmers, watching the skies, are not sure it will be enough.
Weather forecast agencies have warned there could be more floods until the end of November.