It said the magnitude 6.7 quake actually struck west of the Macquarie Islands at a depth of 10km.
GNS duty seismologist Caroline Little said: "The real earthquake was 1000km south of New Zealand. It's a magnitude 6.7 near Macquarie Island.
"This won't have caused a tsunami."
Little said an automatic earthquake location system picked up quake locations within about a minute of one hitting.
"Ninety-five to 99 per cent of the time it's really good at getting accurate locations for New Zealand earthquakes.
"But sometimes with these large earthquakes far outside the New Zealand network, we won't be able to locate the earthquake very well,'' she said.
"But we do pick up the earthquake waves and so our system mislocates that as an earthquake within New Zealand - that's what's happened here."
People were advised to always check the GNS website to see whether the location had been reviewed by a duty officer.
The other tip was to check felt reports. In this case, there were three felt reports in Wellington. However, Little doubted they related to this quake.
"If there was a big earthquake in Otago, we'd expect to see hundreds of felt reports instantly that would match up with that."
The Fire Service said they had not received any reports of quake-related damage and, as yet, had not been called out to any jobs relating to it.
Today's shake comes a week after a 7.1 magnitude strong quake struck the East Cape of the country.