Torrential downpours during the annual rainy season have hit 21 of the country's 37 states, CNN reported Friday.
An estimated 134,000 people have been affected by the flooding, officials said.
"A lot of people have been displaced," said Tam Alazigha, chief economic adviser for low-lying Benue state. "Snakes, crocodiles and hippos have been displaced and are ending up in people's homes. Everyone has been displaced."
With more rain forecast, Alazigha said, authorities are evacuating residents to shelters at schools on higher ground.
On Thursday, President Goodluck Jonathan called a meeting with governors of the affected states to discuss intervention strategies and threats to the nation's food security, The Nigerian Tribune reported.
Environment Minister Hadiza Mailafia said Wednesday more than 5,000 farm plots had been washed away.
Forecasters say the heavy rains may last until the end of November.