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GeoNet cautioned people to be prepared for a significant earthquake on the Alpine Fault, where the quake is thought to have occurred.
The magnitude-5.5 quake at 3.24am was centred about 40km northeast of Milford Sound, at a depth of 5km and was felt across the South.
There were no reports of significant damage.
Southern residents from Queenstown, Wanaka, Cromwell, Clyde, Lawrence, Oamaru and Dunedin posted on the Otago Daily Times Facebook page saying they felt the quake.
Queenstown resident Kamna Nayyer said the earthquake woke her 18-month-old daughter."Our whole house was making a crackling sound and we both were completely shaken. It was scary. I originally thought a big car or truck had hit my house," Mrs Nayyer said
Vivienne Hunt, who lives in Jacks Point, Queenstown, told The New Zealand Herald she was woken up by the tremors between 3.30am and 4am.
"It felt like a large truck passing, causing the ground to tremble and lasted a few minutes," she said.
Wanaka resident Julie Gillan said she woke up to her Venetian blinds and sliding wardrobe door rattling.
Freda Lange, also from Wanaka, described the earthquake as very strong and it lasted at least five seconds.
The quake was part of a swarm of tremors around Milford Sound.
After the quake, GeoNet posted a warning which said the Alpine Fault system had the potential for larger events.
"We would like to make sure that you are prepared for a large earthquake at all times."
The Alpine Fault runs hundreds of kilometres up the spine of the South Island, from Fiordland along the west of the Southern Alps. - Additional reporting NZME