The government estimates that some 2,000 families have already been displaced by flooding caused by heavy rains and it appealed late Monday for immediate help to prevent the imminent spread of epidemics.
The West African region has experienced heavy seasonal flooding in the past few years and about 200,000 people were displaced when their houses were destroyed by similar floods in Benin last year.
"There is urgent need of food, potable water, essential drugs, blankets and treated bed nets," Interior Minister Armand Zinzindohoue said after visiting neighborhoods in the main city of Cotonou that were hit by the floods.
Government officials have warned that the situation may worsen in coming days as the rainy season continues.
Forecasts by the African Center of Meteorological Application for Development for July to September 2009, suggest a high probability of rainfall higher than normal in these countries.
Global aid agency Oxfam warned this week that poor communities across Africa, Asia and Latin America were being hit hard by effects of global warming, with rainfall becoming shorter and more erratic in many places.