The death toll has reached three dozen and is expected to rise in extreme storms along Pacific coastal regions of South America, reports say.
At least 25 people had died during intense rains, landslides and high waves in Ecuador, officials said on Saturday.
Lightning strikes on a police school in the capital Quito injured 52 people, 15 of whom required hospitalisation.
The extreme weather also caused heavy economic damage to farmland and the fishing industry, including boats smashed against rocks and piers, reports said.
In the northern Chilean desert region of Atacama, rare heavy storms caused flash floods and mudslides that killed at least 11 people and destroyed many homes and roads.
"As we go on opening up the routes, there could be a rising death toll, said Ricardo Toro, director of the Office of National Emergencies.
He said there were at least 19 people officially listed as missing, and more than 5000 had been displaced by the destruction.
Local officials also warned that faults in upstream dams could be releasing toxic material from desert mines including arsenic and mercury down on inhabited areas.
They demanded help from the central government to remove tons of mud that accumulated in coastal towns, for fear that it contains dangerous heavy metals.
"That must be done as soon as possible," said Senator Alejandro Guillier, who represents the region around Antofagasta port.
The 700 kilometre-long Atacama desert region between the Andes range and the sea is considered to be one of the driest places on Earth.
"This is the most anomalous event that has happened here," local meteorologist Anthony Sagliani told state television.
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