Last year, similar severe weather caused unprecedented flooding in the southern half of the country, resulting in villages being washed away and many people losing their homes.
According to NEMA, this warning is based on alerts received from the African Centre of Meteorological Applications for Development based in Niamey, Niger Republic.
The center issued the warning on Monday evening to countries in the Central, East and West African sub-regions.
In Nigeria, Lagos and its environs are expected to experience heavy torrential rainfall and the advisory means that all residents must take precautions.
Parents and teachers were especially enjoined to keep watchful eyes on their wards while motorists were warned to avoid driving in the rain, but not to stay inside the vehicle if they decided to park.
NEMA also warned parents to avoid sending their wards on errands during the rains, and to avoid dumping of refuse in the drains.
In the event of unusually heavy accumulation of water, the Agency advised residents to relocate to high ground areas, and to call the nearest police station or the agency on its emergency numbers: 080022636432; 08160581814 or 08067715203.