Gholamreza Shariati, governor of Khuzestan Province, said that he ordered the evacuations as a "precautionary and preventive move to avert any danger", according to the Tasnim news agency.
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Between 60,000 and 70,000 residents will be evacuated, according to estimates.
Torrential rains hit Iran in the last days of March. According to Iranian officials, the floods affected about 400 settlements located in 15 provinces in the north of the country.
Because of the rampant disaster, more than 2,300 roads were blocked, while at least 84 bridges were destroyed and 141 rivers overflowed their banks. In addition, since the beginning of the hazardous weather, more than 400 landslides have been recorded.