Kiwirail has not yet confirmed the cause of a "spectacular" train derailment in North Otago at the weekend.

On Saturday, a spokeswoman for KiwiRail confirmed an investigation into the non-injury crash was under way.

"We do have derailments from time to time," the spokeswoman said.

"We'd actually been through quite a long period without one. This is the first one in nearly seven months. It sounds like it's rather a visible one.

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"I haven't seen it, but it's apparently quite spectacular."

When the freight train came off the rails near State Highway 1 at Waianakarua at 2am on Saturday, there was a "horrible ... screeching, scraping noise", the owner of The Mill House said.

Malcolm Fagerlund said he did not see the crash, but he heard when the overnight freight service, which left Christchurch bound for Invercargill, lost three wagons and derailed next to his property.

Lights were flashing at the nearby railway crossing for an hour after the derailment, and Mr Fagerlund said his guests were relieved to hear in the morning the train driver was not injured.

The train lost the wagons after crossing a short bridge over the Waianakarua River.

The KiwiRail spokeswoman said three wagons left the track, but the locomotive did not, and the driver was "fine".

The wagons, "the first three of the last six" on the 17-carriage train, were not carrying dangerous cargo, she said.

There was minor damage to the track.

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A KiwiRail employee at the site on Saturday said the wagons blocking the railway tracks would be moved to either side of the tracks to allow service to return to normal, but would remain at the site for a few days before they were removed.

Mr Fagerlund said the derailment had occurred near where contractors had been working, and speed restrictions had been in place until Friday.