Some 800 residents have been displaced and at least two people injured by the torrent of rain that struck Punta Arenas overlooking the Strait of Magellan, The Santiago Times reported Wednesday.
The actual level of rainfall reached 5.2 inches in some areas, meteorologists said, even though only an inch of rain was forecast.
The regional director for Chile's National Emergency Service (Onemi) has been dismissed for the service's failure to raise the alarm leaving thousands of residents unprepared for the intensity of the storm.
Labor Minister Evelyn Matthei said "the government has totally restructured Onemi."
Matthei arrived in the area Tuesday to supervise rescue and recovery efforts.
In Chile's northern Arica province, flooding along the San Jose River has displaced some 300 residents.