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A police spokeswoman said they received reports of the incident on State Highway 1, between Double Hill Rd and Manse Rd, shortly after 5.15pm and advised KiwiRail.
Police said they believed there was just one person in the ute and no other vehicles were involved. It was not known if the driver was injured.
A KiwiRail spokesperson said at 8.30pm the line was expected to be reopened shortly, once the vehicle was clear of the track and the track had been inspected.
She said only one south-bound train had been affected. It had arrived at Merton, where it was being held until the line was reopened.