The earthquake of magnitude 6.8 on the Richter scale occurred near the west coast of the South Island, one of the two largest that make up the country.
The agency said in a statement that strong currents and swells can cause injuries and drowning.
The current sea conditions pose a risk to the lives of swimmers, surfers, fishermen and anyone in the water or near the shore.
Those in or near the sea should stay out of the water, away from beaches and coastal areas and away from harbors, marinas, rivers and estuaries, the statement said.
The areas of the west coast of the South Island from Milford Sound to Puysegur Point are on alert for this adverse behavior of nature and the occurrence of a tsunami is not ruled out.
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