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There were 28 aftershocks in just over six hours on Monday night, following a 5.5 magnitude earthquake 15km north of Milford Sound.
No significant damage has been reported so far and while the earthquake, which hit at 10.35pm, triggered three avalanches at the Homer Tunnel, debris did not make it to the road.
GeoNet initially reported the earthquake as a 5.5 magnitude, then upgraded it to a 6.3 before downgrading it again.
The largest aftershocks measured 3.7 - one of that magnitude was recorded at 10.40pm on Monday and another at 1.48am yesterday.
Almost 7000 people, largely across Otago and Southland, reported feeling the first quake, which was also felt as far north as Auckland.
In Queenstown residents reported feeling the earthquake - strong enough to knock items off shelves - in two waves, lasting about a minute.
A FreshChoice Queenstown employee said some stock fell from shelves in the Gorge Rd supermarket, which was still open at the time.
''It did definitely rattle and some things fell off the shelves ... we were surprised that none of the wine was broken.
''A little jar here and there broke open, but no major damage.''
Emergency Management Southland manager Angus McKay said he was in Invercargill when the earthquake hit but ''was one of the ones who didn't feel it''.
''It all depends on where it is and what depth it is - that's where the geology of Southland and Otago comes into it, so, you might feel it really strongly in Queenstown, but you might not feel it at all in Winton, or vice versa.
''It's just one of those quirky things, really.''
He said the Milford Fire and Emergency team was activated and investigated but found no damage.
''I think it was just a really big shake that gave everyone a bit of a scare.
''What we're trying to say to people is we're living on a plate boundary, in the middle of the sea.
''We should just expect earthquakes, because they're going to carry on.
''Really, rather than being surprised about it, it's about being prepared for it.''
There was also no tsunami risk on Monday night - Mr McKay said Milford Sound was ''a little unusual'' and the tsunami risk did not come from the ocean, but from an earthquake triggering a big enough rock fall to cause a ''very localised wave'' in fiords or lakes.