"KiwiRail has begun an investigation," a spokesperson said.
"We are naturally shocked by this event and have begun an immediate investigation into what happened," KiwiRail chief operating officer Todd Moyle said.
"For some reason, the shunt locomotive, pushing the wagon, has travelled across the marshalling yards to a linkspan – a ramp that connects the land to a ship – and fallen in to the water."
KiwiRail confirmed a linkspan (a ramp between the land and a vessel) was damaged.
"KiwiRail is working with other agencies on safely managing the situation, and recovery of the wagon and locomotive."
Police were notified at 3.30pm that a "train had gone into the sea", however Police were not required at the scene.
Police have since been advised by KiwiRail that it was a "remote-controlled shunter train" with nobody on board.
KiwiRail inspected the water tonight and found that the diesel tank, and the tank containers remain sealed and intact.
The port has partially reopened. Interislander services are due to resume tonight.