Copiapo: The death toll - a 34-year-old man and a 45-year-old woman - was provided by Deputy Interior Minister Mahmud Aleuy.
Chile rushed in the army and urged people to flee as heavy rains flooded towns.
The torrential storms, which began late Tuesday and are unusual for the arid region, have left 700 people homeless, cut off roads, caused power outages and severed communications.
"Anyone in an at-risk zone in the Atacama region should evacuate. What we need is for you to get to safety," warned Interior Minister Rodrigo Penailillo.
President Michelle Bachelet traveled to the region to coordinate relief operations.
About 40,000 people were without electricity and as many or more without potable water, officials said.
The rain flooded the main streets in the regional capital Copiapo and in several towns. It also cut off hundreds of residents in remote areas.
The weather forced state-owned Codelco to halt operations in Atacama and the neighboring region of Antofagasta.
"At this time, Codelco's operations are resuming slowly, as we constantly monitor weather conditions to ensure the safety of our people and equipment," said the company, which produces around 11 percent of the world's copper - 1.6 million tons a year.
Flights were delayed at the Calama and Antofagasta airports, hubs for the area's mining operations.
Authorities declared a health alert for several municipalities.
Bachelet expressed solidarity with all those affected and said her government would send all necessary resources to the area.
The floods in the north came as southern Chile battled devastating wildfires exacerbated by a severe drought.
Flooding caused by torrential rains in a normally dry region of northern Chile left at least two people dead and 24 missing on Wednesday, officials said.
The disaster in the Atacama area prompted the government to declare a state of emergency, which means the military take charge over civilian leaders.
It also forced a suspension of operations by Codelco, the world's biggest copper producer.
Chile rushed in the army and urged people to flee as heavy rains flooded towns.
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"Anyone in an at-risk zone in the Atacama region should evacuate. What we need is for you to get to safety," warned Interior Minister Rodrigo Penailillo.
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About 40,000 people were without electricity and as many or more without potable water, officials said.
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The weather forced state-owned Codelco to halt operations in Atacama and the neighboring region of Antofagasta.
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Flights were delayed at the Calama and Antofagasta airports, hubs for the area's mining operations.
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Bachelet expressed solidarity with all those affected and said her government would send all necessary resources to the area.
The floods in the north came as southern Chile battled devastating wildfires exacerbated by a severe drought.
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