The Nigerian Meteorological Agency (NiMet) said "conditions are highly conducive for intense and prolonged rainfall, which, when combined with already saturated soil profiles and elevated river levels, significantly increases the risk of flooding".
The weather agency flagged several "high risk" states, including Niger State, where floods flattened a neighbourhood and killed at least 200 in May.
Although not on the warning list, more than 10 hours of heavy rainfall on Monday flooded several areas in the commercial hub Lagos of around 20 million people, where officials warned residents in "lowland" areas to evacuate.
"Based on the predictions from NiMet, we are going to have much more rains this year than we had last year," Tokunbo Wahab, Lagos state commissioner for the environment, told local broadcaster Channels Television.
"For those who stay in the lowland of Lagos, they may have to move to the upland pending when rain recedes," he said listing some popular neighbourhoods such as Lekki and Ikorodu.
Heavy rains sweep Nigeria between June and November, often triggering dangerous floods where poor infrastructure and inadequate drainage often worsen the impact across Africa's most populous country.
In 2022, more than 500 people died and 1.4 million were displaced in the country's worst floods in a decade, while last year more than 300 people were killed and over a million displaced in at least 34 out of Nigeria's 36 states.
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