A TAIC spokesperson said investigators were now in a rush to gather as much evidence as possible before the flooding disappeared.
"The commission's investigators arrived at the accident site early on Tuesday afternoon and have commenced their initial work recording the accident scene and gathering evidence that could disappear or change – such as the effects of weather and flooding."
A protection order was put in place on the track from 2km of the crash site at either end. That order has since been partially lifted.
The commission said KiwiRail was actively assisting in "this complicated investigation".
"TAIC's evidence gathering is broad to support the many routes that an investigation could follow. Our investigators will be interviewing railway staff, inspecting the rail and rolling stock, and the operator's safety systems for managing hazards and mitigating the risks of flooding."