The robotic sub, on loan from Sweden, is exploring the Kaikōura Canyon, which is about 60km long and 2000 metres deep.
The undersea area was transformed during the 2016 earthquake, when about 850 million tonnes of sediment cascaded through the canyon.
A Niwa spokesman says it triggered landslides that collected a huge amount of mud which flowed out of the canyon and travelled at least 600km along the seafloor.
The landslides could have generated a tsunami.
The battery-powered sub uses sonar to help scientists build a clearer picture of how the seabed reacted to the quake.
Scientists have about a month to use the sub before it is returned to Europe.
It will also provide insight into how marine life is recovering four years after the habitat was changed forever.
