The 5.2 earthquake caused strong shaking near Cheviot just after 8am.
It hit 20km southwest of Cheviot at a depth of 12km and has been described as causing strong swaying.
Within minutes nearly 1100 people had reported feeling it across the upper South Island.
Robin McCarthy, who was on the third storey of a building in Hereford St in Christchurch, told the ODT it was a "roller" rather than intense shaking.
''The building creeked and it lasted longer than most aftershocks. I wonder whether it was another faultline rupture rather than movement on a recently ruptured faultline.''
GeoNet said the severe quake was part of the 7.8 Kaikoura aftershock sequence.
The region has escaped major damage from either quake and the Fire Service said it had no callouts as a result of today's tremors.
Cheviot woman Jane Thompson said the latest frightening quake had her heading for cover.
"As soon as it started I leaped under my desk and my dogs joined me," she said.
The latest tremor followed a strong, shallow quake that struck Canterbury before dawn, jolting people awake across the South Island.
GeoNet says the first quake, magnitude 4.7, struck at 5.17am.
It was centred 20km southwest of Cheviot and just 9km deep.
Nearly 500 people from Christchurch to the Manawatu reported feeling the first tremor, and most were woken from their sleep.
Many described it starting with a loud crack followed by a bed-shaking wobble.
Some called it yet another setback after last year's Kaikoura 7.8 quake.
Waiau resident Jenny Holt posted on the GeoNet Facebook page: "My three kiddies terrified and crying in my bed now."
Jenna Wood wrote: "Heart racing. Stupid quakes bugger off! Felt in Woodend."
"Car shaking in Hornby felt as If was rolling," wrote Haydz Cranefield.
