Residents reported hearing a thunderous bang, about 7:20pm on Saturday, between Box Hill and Khandallah stations and emergency services rushed to the scene.
Police said six people were injured and taken to hospital by ambulance, although Wellington Free Ambulance told RNZ eight people were hurt.
Two people were in a serious condition on Saturday night.
KiwiRail's chief metro officer David Gordon said work was under way to find out the cause of the "gut-wrenching" incident.
"Firstly, thoughts go out to those people [involved] ... even if they are not hurt, they'll be in some form of shock I would imagine."
One of the injured was the train driver, who hit his head in the crash.
Gordon said the collision happened where double tracks merged into single tracks. The train had come to rest against a block of concrete designed for that purpose.
"It's still standing upright but its wheels are off the tracks."
The train would not be moved until the Transport Accident Investigation Commission (TAIC) and New Zealand Transport Agency investigators had been on site.
"If you were standing up, you would have been thrown forward; if you're sitting down ... I don't know."
He said he would "like to get to the bottom" of the incident soon.
Louise Cook, chief investigator at the Transport Accident Investigation Commission (TAIC) said investigators began working at the site overnight. They would like to hear from any witnesses.
"Getting information is vital so we're keen to hear as soon as possible from people who were on the train or who saw the accident occur. We're especially interested in receiving photos or videos."
Jo Hosie, who saw the aftermath, rushed to the scene after finding out her friends were on the train.
She saw multiple people injured.
"We've seen them all getting carted to the ambulance on the stretchers and that," Hosie said.
It was not determined yet if the crash was a derailment or not, Chairman of Greater Wellington Regional Council, Daran Ponter, said.
"I am aware of speculation in the community that the accident is the consequence of a derailment. But this is only speculation.
"All we can say is that the trains crashed into concrete blocks at the end of a runoff section of track. These concrete blocks are designed to stop trains progressing further. They were installed in 2025 as part of a KiwiRail upgrade programme."
However, police on Saturday said the crash was a derailment.
