In a statement, INAM said Gaza, Inhambane and Maputo provinces should brace for heavy rains ranging from 50 to 100 millimetres between Friday afternoon and Sunday.
The rains are expected to be accompanied by gusty winds of up to 70 kilometres an hour and trigger waves as high as five metres in some areas, raising fears of destruction of property and injuries to people.
The capital Maputo and the neighbouring Matola city are among those expected to be affected by the heavy rains.
Mozambique is prone to flooding this time of the year due to the frequency of cyclones and other storms emanating from the Indian Ocean.
Cyclone Eloise, which hit southern parts of the country and neighbouring South Africa and Zimbabwe last month, displaced about 43,000 families and flooded thousands of hectares of land in Gaza province, according to the National Institute for Disaster Risk Management.