The floods have affected some major rice producing states, the minister said in Abuja, Nigeria's capital, adding that the country might experience a scarcity of rice, if the issue was not addressed.
"We have to find out a way to assist farmers, who were affected by the flood," he told a meeting of farmers.
"There are different varieties of rice that are being produced at National Agricultural Seed Council like faro 66 and 67, which are flood tolerant," he said.
"We hope to get them into the field in large quantity for farmers to plant in the near future," the minister said.
Heavy rains have been hitting Nigeria since late July, triggering massive floods in some states.
Livestock and other properties, including some 100 hectares of farmland, were either washed away or submerged.
Meteorologists forecast the heavy rainfall would continue in large parts of the country over the next few weeks.
According to the latest data by the National Emergency Management Agency (NEMA), at least 108 people were killed by the flood and 192 others wounded.
Sanni Datti, the spokesman for NEMA, confirmed to Xinhua that some 122,600 hectares of agricultural land were damaged and more than 13,000 houses had been destroyed by the devastating flood.