Authorities said they were not yet declaring a national emergency, saying the regions are coping well.
The magnitude-7.8 quake struck just after midnight 132 miles south of Wellington, where it collapsed a ferry loading ramp, broke windows and caused items to fall from shelves.
Authorities later downgraded tsunami warnings around the country following the quake.
The Ministry of Civil Defence and Emergency Management reported that a tsunami wave struck at about 1:50am and warned residents living in low-lying areas anywhere along the country's east coast to move to higher ground.
Prime Minister John Key said at a news conference later that the tsunami warnings were being downgraded to coastal warnings.
Speaking about six hours after the quake struck, Mr Key said he was unable to give further information on the fatalities until authorities had confirmed all the details.
He said officials had no reason to believe the death toll would rise.
"On the very best information we have at the moment, we think it's only likely to be two. But of course there are isolated parts of the country which we don't have perfect eyes on, so we can't be 100% sure," he said.
Mr Key said that crews would better be able to assess the damage during the day. He said officials had decided not to declare a national emergency because the nation's regions were able to adequately cope with the situation.
He said waves of about two metres had hit the coast, but the tsunami threat had since been downgraded to coastal warnings.
The quake temporarily knocked out New Zealand's emergency call number, 111, police reported.
Authorities in Wellington were urging people who work in the centre of the city to stay home on Monday.
City officials said that some large buildings were showing signs of structural stress, and the quake would likely have caused a mess in some buildings.
The city's rail network was shut while crews checked tracks, bridges and tunnels.
The quake brought back memories of the magnitude-6.3 earthquake that struck Christchurch in 2011, destroying much of the city centre and killing 185 people.
New Zealand, with a population of 4.7 million, sits on the "Ring of Fire," an arc of seismic faults around the Pacific Ocean where earthquakes are common.