According to GeoNet, the quake hit 35 km north-west of Kaikoura at a depth of 84km.
The quake follow a magnitude 4.3 shake and a 5.2 in Wellington and Seddon yesterday.
Both quakes were 24 kilometres deep.
A NZ Herald reader Paddy Brocherie wrote in to describe the quake as "the longest quake I've ever felt and I live in Christchurch".
"Bad, bad, bad."
Meanwhile, Spark is experiencing network trouble following the shakes, according to a tweet the company posted this afternoon.
Public information specialist for GeoNet, Caroline Little, said the magnitude 6.4 quake was centered 40km north west of Kaikoura.
She said those in Kaikoura were sure to have felt the tremor.
"The deeper the quake, the more rolling the shaking is rather than that violent shaking - they definitely would have felt it."
Ms Little said there were reports of the quake being felt as far south as Timaru, and as far north as Hamilton.
She said this was for "light shaking".
It was likely the quakes were related to two quakes that shook the country yesterday, Ms Little said.
Yesterday's quakes were located east of Seddon, Marlborough, and were widely felt across the strait in Wellington.
The first came at 10.36am and was recorded 20km east of Seddon. It was 23km deep and had a magnitude of 4.4, GeoNet said.
The second hit six minutes later at 10.42am and was more intense and prolonged than the first.
It was recorded 15km east of Seddon, had a magnitude of 5.1 and was described as strong by GeoNet.
"I'd say that these are all related in that area and are related to the 2013 quakes as well around the Cook Strait and Seddon area," Ms Little said.
