What was first thought to have been a big East Coast earthquake actually turned out to be two others that struck elsewhere and within minutes each other, confusing GeoNet's automated system.

GeoNet first reported a single earthquake striking near Ruatoria just after 8pm last night.

But seismologists who checked the data soon found there had been two events: one 4.7 quake that hit 5km north of Whanganui, and another 5.1 event recorded in the Kermadecs, far above New Zealand, minutes earlier.

"By the time the waves travelled from the Kermadecs to the GeoNet network, shaking was also coming from the Whanganui event, and that got combined and the automated system located it as a magnitude 6 event in Ruatoria," GNS Science seismologist Matt Gerstenberger said.

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GeoNet's system – combining more than 190 seismographs and 270 strong motion sensors – worked by calculating how fast earthquake waves travelling through the Earth's crust turned up at different parts of the network, and then triangulating back to the source event.

It wasn't rare for the system to get confused by multiple events, but it was uncommon: Gerstenberger said such incidents happened a few times each year.

"You can see a map that shows where the shaking is happening in real time – and if you looked at immediately where this was happening, it was around Whanganui, not the East Cape."

Thousands of people reported feeling the Whanganui quake.