More downpours are forecast for the south-west, with 400,000 people at risk. Dangerously full dams are being opened to ease water build-up.
Women and children are being moved to safer areas while men have been asked to stay to assist with relief efforts.
Where are the latest evacuations?
The south-western province of Khuzestan, which borders Iraq, is the main focus.
Six towns and cities along the Karkheh river needed to be evacuated as soon as possible, Khuzestan's governor Gholamreza Shariati said.
He said the situation was critical and, despite the fears of renewed flooding, the Karkheh dam was being opened to release build-up.
Around 70 villages in the province have been evacuated in the past week. There is no order of evacuation yet for Khuzestan's capital, Ahvaz.
Iraq on Saturday closed its Sheeb border crossing to both travellers and trade until further notice.
Energy companies in the oil-rich region have helped the relief effort by using pumps to remove water.
Where else has been affected?
Severe flooding began hitting the north-east, particularly Golestan on the Turkmenistan border, on 19 March.
On 25 March, the west and south-west were struck, with more rain in the same area on 1 April. Lorestan province was the worst hit then, with cities and villages cut off.
Some 12,000km (7,500 miles) of road, more than a third of the country's network, has been affected.
Thousands of roads, bridges and buildings have been destroyed.
So far, 86,000 people are living in emergency shelters, 1,000 of whom were airlifted to safety.
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