As dawn broke there was scant information from many rural villages in the South Island, which were isolated by landslips and fractured telephone communications as strong aftershocks continued for several hours.
Prime Minister John Key confirmed two people had died and said "we cannot rule out" that number will rise, nearly seven hours after the main quake.
He added that the tsunami warning had been downgraded.
Mr Key says a Defence Force helicopter will be sent to Kaikoura after road access to the coastal town was cut off by slips, while schools and early childhood centres from Wellington to Canterbury will remain closed until they've been assessed and some areas remain without power.
Police had been trying to reach the scene of one fatality at a remote property 150 kilometres north of Christchurch while another person died in a historic homestead which collapsed at the nearby fishing village of Kaikoura.
"At this point we are unable to give precise details of what caused those fatalities," Key said, adding that communication problems made it difficult to get information.
Helicopters were taking officials workers to the worst-affected area, he said.
"As soon as we can get a much better assessment of the actual damage then we can work out the next steps.
Homes were damaged in North Canterbury, and there were also landslips and bridge damage, cutting off Hanmer Springs, which was at the quake's epicentre.
A train bridge at Wellington's ferry terminal also collapsed, and there was also damage to buildings around the capital's central business district.
Mr Key said that "it was the most significant shock I can remember in Wellington.
"There will be quite major costs around roads and infrastructure."
