GeoNet reported the "strong" quake struck at 10.35pm at a depth of 12km and was centred 20km northwest of Milford Sound.
Nearly 7000 people reported feeling the quake.
Milford Road Alliance manager Kevin Thompson said State Highway 94, between Te Anau and Milford Sound, was inspected this morning and ''no major damage'' has been found.
The highway was closed last night due to snowfall - it reopened just after 10am.
"Three avalanches at the Homer Tunnel were triggered at the time of [the] quake, however, no debris made it to the highway.
"Overall, the avalanche hazard remains low, based on the monitoring equipment data the Milford Road Alliance has in place, combined with specialist review and assessment by the avalanche technician team over winter.''
Initially reported as a 5.5 magnitude, then upgraded to a 6.3, it has since been revised back down, although GeoNet said they were assessing the shake and would provide a final magnitude.
"We are in Mosgiel...I was just turning the radio back on. I lay back down and thought 'oh my god', the bed was going from left to right," talkback caller Kerry told Newstalk ZB's Marcus Lush.
"It was really really strong in south Dunedin," said another caller, Nancy. "Quite frightening."
"It's scary," said a third caller.
Emergency Management Southland said the Milford Fire and Emergency team had been activated following the quake and were investigating, but had not yet received any reports of damage or injuries.
It had since given an update, saying "things are calming down a little in Milford - everyone a little shaken up, but OK".
Milford Sound Infrastructure's Philip King told RNZ he could hear small debris falling off the mountains, but nothing big enough to make them worry about a tsunami.
He said they were all shaken up, but the earthquake was reasonably moderate compared to what it could have been.
King said the whole community was on lookout, with everybody monitoring radio and working as a team, and they were now on watch for aftershocks.
A Queenstown resident said the shaking lasted a minute and was strong enough to knock items of shelves.
She said the quake came in two waves with the first lasting about 15 seconds, followed by a longer one which lasted about 45 seconds.
It was strong enough that she felt the need to shelter under a doorway. "I ran for the door."
It was the strongest quake she had felt in the area since at least 2007 when a 6.7 magnitude quake struck in George Sound, Fiordland.
The quake was also felt at the Otago Daily Times newspaper office in Dunedin and in Invercargill.
A police spokeswoman said there were no reports of damage from the quake.
ODT readers reported feeling strong shaking across Otago and Southland and less than 30 minutes after it struck nearly 7000 people have reported feeling the earthquake on GeoNet.
In the 20 minutes following the shake, another four weaker earthquakes measured between magnitude 2.9 and 3.7 shook the same area, north of Milford Sound.
With NZME
