About 76 people have died in flooding in the country since August, The Guardian newspaper reported from Lagos.
The latest flooding drove thousands of people from their homes and emergency management officials expected conditions to worsen.
There was extensive flooding along the banks of the Benue and Niger rivers and their tributaries in the southwestern states of Benue and Kogi.
The Nigeria Red Cross Society said Sunday it had deployed three boats to riverine areas of Kogi State to rescue trapped flood victims. The Nigerian navy is involved I similar operations.
Cars caught in flooding on a highway between the Nigerian capital of Abuja and Lokoja, the capital of Kogi state to the south, formed a line about 9 miles long.
Six states covering virtually the entire coast of Nigerian from Lagos to Calabar have been severely affected by flooding.
A presidential committee set up to assess the damage says the flooding is the worst the country has experienced in 29 years.