New Zealand lies on the Ring of Fire, a horseshoe-shaped area surrounding almost the entire Pacific Rim that is known for frequent earthquakes and volcanic eruptions.
GeoNet, which monitors seismic activity in New Zealand, said the two quakes were "separate but related," and that the combination of the two lasted about two minutes.
"It's quite a complex quake," said Caroline Little, a spokeswoman for GeoNet. "It looks like two events happening almost simultaneously."
Kaikoura's telecommunications, water and power supplies were cut off Monday when landslides blocked the main road to the town, which is popular with tourists and has a population of about 3,600.
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Infrastructural damage will likely be the biggest issue facing the region, and Prime Minister John Key said he believed the number of fatalities would remain low.
"In the short term what we're trying to do is make sure that the people of Kaikoura and the likes have food, water, help and backup," Key said in a video posted to Twitter. "I'd say it's billions of dollars worth of money that we have to spend here but we're focused on what we're doing and we'll keep up the good work."
It could take days to evacuate the hundreds of people stuck in the town. Beginning Tuesday, the military plans to use four NH90 helicopters, which can each transport about 18 people out of the town at a time.
Aftershocks from the South Island were felt all the way in Wellington, the country's capital on the North Island. Residents were advised to remain indoors as workers cleared debris and checked buildings.
Christchurch is still recovering from a 2011 earthquake that killed 185 people and destroyed the city center, causing $25 billion in damage. Though Sunday's quake was much stronger, the damage was reduced because the tremor's epicenter was in a rural area.