Today's deadly Christchurch earthquake could be a sign of further devastation to come, with one seismologist warning that it had increased the likelihood of a large earthquake hitting Wellington.

Seismologists expected an aftershock as big as today's 6.3 magnitude quake would follow the 7.1 magnitude quake that struck Canterbury on September 4, but thought it would strike much sooner.

Australian seismologist Kevin McCue, director of the privately-owned Australian Seismological Centre, said geological activity was impossible to predict, "but it tends to occur in clusters".

"If you have one (quake) it ups the hazard," he said.

The Canberra-based seismologist, also an adjunct professor at Central Queensland University, said the quake would have had some impact on the boundary between the Australian and Pacific tectonic plates.

The fault runs up the South Island's West Coast, across the Cook Strait, under Wellington and up the east coast of the North Island.

"This quake has the potential to load up the plate boundary, increasing the likelihood of a quake at Wellington," he said.

"Wellington has always been considered much more at risk (than Christchurch) because it straddles the plate boundary.

"New Zealand has been relatively quiet since the 1930s -- maybe we are about to catch up."

John Ristau of the Institute of Geological and Nuclear Sciences (GNS) said today's quake at 12.51pm was still classified as a large aftershock in seismological terms.

However, it felt stronger to many in Christchurch than the September quake as it was shallower - 5km compared with about 10km in September - and its epicentre was closer to the city, at 10km southeast of the city, compared with 30km west of the city around Darfield in September.

"Right from the start we've said that the general rule of thumb for major earthquakes like the Darfield earthquake is that the largest aftershock is about a magnitude unit smaller than the main shock," Mr Ristau said.

"Up until this point we hadn't seen that magnitude six aftershock, and we kind of hoped that by now it wasn't going to happen anymore.

"It's a very big aftershock, but it's still an aftershock."

Mr Ristau described today's shock as "very shallow" and said the fact it was closer and shallower would explain why the damage in some parts of Christchurch was greater than in September.

"It's closer, plus if you had buildings that were already weakened by the 7.1, then one like this would come along and finish the job."

A swarm of large aftershocks has followed today's 6.3 magnitude quake.