In telephone conversations with a number of officials on Friday, President Rouhani issued orders for relief aid in the areas that have been afflicted by the severe weather, and for estimating the destruction the flooding has wreaked on the western regions.
Vice President Mohammad Baqer Nobakht on Friday paid a visit to Ilam, a province severely affected by flooding from hours of relentless, saturating rains.
Flashfloods brought dozens of cities in eight western provinces to a standstill on Wednesday and Thursday, sending normally tame rivers past their banks and inundating streets and homes.
The pouring rain in the mountainous province of Ilam has been reported as unprecedented in a century.
Six people have died in the flooding.
State officials had already warned of a strong El Nino system that would cause a severe frost with heavy wintry showers.
Earlier this month, Energy Minister Hamid Chitchian issued a letter, warning of an El Nino weather system that is expected to pummel the country with torrents of rain and cause flooding and freezing temperatures in autumn and winter.