Two-metre high waves have hit Chile's northern coast following an 8.2 earthquake in the country.
Officials said the five killed included people who were crushed by collapsing walls or were killed by heart attacks.
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The country's top defence officer said the force may ignore any order to launch a nuclear attack which is deemed to be illegal.
Navy officials say they have received seven short satellite calls which are though to have come from the submarine.
The President is to meet with with the army commander who put him under arrest as he resists calls for him to stand down.