The earthquake, which hit at 6.48am, was swiftly followed by more than 30 aftershocks - the largest measuring 4.2 in magnitude, which hit at 6.59am, 30km south west of Arthur's Pass.
Nearly 3000 people have reported on the GeoNet website feeling the quake, from Mandeville in Southland to the central North Island.
While the tremor had been categorised as severe, its isolated location meant no injuries to people or property damage had been reported.
GNS seismologist John Ristau said it was not unusual to have earthquakes of this size in the area.
"We've had them in the past century, there have been at least a couple of others that have been above magnitude 6."
Aftershocks would go on for a while yet, which could reach the magnitude 5 range, he said.
"Just be aware there could be a sizeable aftershock coming - but beyond that we can't say for certain whether there'll be anything bigger coming."
Roading and rail companies have been assessing if there was any damage to the country's infrastructure.
The New Zealand Transport Agency said it had been checking all state highways in Canterbury and the West Coast for any damage from the tremors.
"Our contractors have checked State Highway 77, near Methven, State Highway 73 through Arthur's Pass, and State Highway 6 on the West Coast.
"There are no reports of any damage."
A KiwiRail spokeswoman said some South Island rail lines had been closed and were being inspected by KiwiRail staff.
Lines were closed between Oamaru and Christchurch, Oaro (south of Kaikoura) and Christchurch, along with the Midland and Stillwater lines.
Freight services on those lines had been suspended, along with the TranzAlpine. Bus replacements were being provided for passengers, she said.
The Coastal Pacific was running but it had been delayed by about 90 minutes.
Services on the lines would resume once they had been inspected and a safety clearance had been given, the spokeswoman said.
A St John spokesman said there were no injuries to staff and no damage to the organisation's premises in Ashburton, Methven, Mayfield, Darfield, and Arthur's Pass.
New Zealand Herald readers have been sending in their experiences of the earthquakes.
Tony Foote said the quakes were "disturbing".
"It rolled on a bit, quite heavily and I felt a bit sea sick as my chair moved about. A bit like being on a rising and falling wave in a small boat.
"There was a worry it might be something bigger on the way as an ornament I hung to see when quakes were happening swung 100mm side to side for several minutes, and the water in my cat's bowl moved up and down 20mm or so."
Graham Walker said he felt the quakes in Timaru.
"As I was eating breakfast house was rolling around for about 10-15 seconds."
Others took to social media to describe the quakes.
Brian Feary tweeted: "Big earthquake here in Arthur's pass! My dog ran in from outside and jumped on bed... No damage so far #eqnz".
A user called The Queen of Cobden wrote: "That #eqnz just felt like the house was at sea (in Christchurch)".