The emergency meeting, slated for Thursday afternoon in Tehran, will be chaired by First Vice-President Eshaq Jahangiri.
It will discuss plans for providing flood relief assistance and helping the flood-stricken people.
Heavy rain and major flooding hit the provinces of Lorestan and Ilam in the west and Khuzestan in the southwest of the country on Thursday.
There has been no reports about the scale of damages or whether there have been any casualties.