"Anyone entering the rail corridor is putting themselves in serious danger," he said.
The main north line was closed to rail services, but work trains, tampers and hi-rail vehicles were operating on the line as part of the recovery.
He said even staff, who were familiar with the area, were not entering tunnels or crossing bridges without a safety plan and continuous monitoring.
"We strongly advise people refrain from entering any railway land. It is not only incredibly dangerous, but illegal under the Railways Act and trespassers can be fined," he said.
KiwiRail would not discuss what goods were on the train, citing commercial sensitivity.
When asked what security measures were being put in place for the train, a Kiwirail spokesperson said the train was stopped during the earthquake as a matter of process and the driver airlifted out of the area.
"The train remains in a remote and dangerous location where safety concerns for our staff, and the equipment that would be required to release the goods from the train, have prevented their wholesale removal.
"KiwiRail is working with local authorities including Civil Defence and the police on how to manage the situation and ways to secure the site. The goods remain the property of our customers and we are working with them on best way to recover them.
"It is profoundly disappointing to KiwiRail that some New Zealanders have looted the train during a natural disaster's aftermath."