The districts have an estimated population of between 60,000 and 70,000.
Iran ordered tens of thousands of residents of the southwestern city of Ahvaz to evacuate immediately on Wednesday as floodwaters entered the capital of oil-rich Khuzestan province, state television reported.
The province's governor, Gholamreza Shariati, said he ordered the evacuation of five districts as a "precautionary and preventive move to avert any danger," Iran's Tasnim news agency reported.
Shariati asked young men to "help us in building dykes and to assist in the evacuation of women, children and the elderly."
"The Dez and Karkheh rivers have for the first time joined each other near Ahvaz and are now flowing towards the city," Shariati told state TV, adding that this was unprecedented.
"These two rivers are far away from each other, but the huge volume of floodwater caused them to join up."
Shariati said a sixth district was also put on standby for possible evacuation.
Khuzestan province has been struggling with major floods due to heavy rains as well as floodwater coming from the north.
It is the latest in a series of unprecedented floods that have hit the normally arid country since March 19, killing at least 70 people.
The country's northeast was first swamped on March 19 before the west and southwest of the country were hit on March 25.
On April 1 the west and southwest were again swamped by floods when heavy rains returned to the area.