"None of the wagons have tipped over onto their side but with one of the wagons, two containers that were on it have toppled off."
The speed limit at the site was 25 kilometres per hour.
It was the second derailment in Hamilton in as many years but Ms Austin said there had been no "significant" recent derailments across the North Island.
She said it was too early to speculate what caused the derailment and that such incidents had been trending down since KiwiRail began putting money into track and wagon upgrades.
"The two main causes of derailment are tracks not up to scratch or old wagons that break down because of their age. Having eliminated a lot of the worst of those two situations the derailment figures have been trending in the right direction."
She added that KiwiRail had been "doing a lot of work in the past 18 months to two years" to remove decaying wooden sleepers from its tracks.