GeoNet said the 20km deep quake struck in the same location as the initial quake. It was reportedly felt in the upper South Island and the Hutt Valley.
Other aftershocks were described by GeoNet as "unnoticeable".
GNS Science seismologist Anna Kaiser said increased seismic activity was excepted in the region in the next few days.
"They will taper off over the next few days - there will be much fewer than there have been today. We always get a level of background activity in this area anyway, so we do expect small quakes for a while."
More than 6000 people had reported feeling the main earthquake, from as far north as New Plymouth to Canterbury in the south.
Earthquakes also struck overnight on the East Cape of the North Island and in the Tasman region.
GeoNet said a magnitude 4.5 quake struck 15km southeast of the East Cape town of Te Araroa at 11.42pm.
The 57km deep quake was described as light in intensity.
Fifteen minutes later, a 3.7 magnitude quake struck 30km west of Murchison in the Tasman region.
GeoNet described the 12km deep quake as moderate.