A wagon of a loaded coal train derailed on Tuesday night, damaging a section of the Midland Line track near the Ōtira Tunnel.
The train was brought to a halt inside the tunnel while heading to Christchurch at around 10pm following the incident.
it was not yet known what caused the derailment.
No injuries were reported, but KiwiRail general manager of engineering and asset management, Lynne Morton said the line would need fixing.
"The derailment has affected a section of track, and KiwiRail teams are assessing the extent of the damage and the repairs required," Morton said.
"We are working to restore the line as quickly and safely as possible."
As a result, TranzAlpine services were impacted, with Wednesday morning's route terminating at Arthur's Pass.
Morton warned railway users that delays and schedule changes were likely to continue, but urged passengers not to worry.
"TranzAlpine services are likely to be affected for the next few days," she said.
"Affected passengers will be contacted directly and offered rebooking or refund options. Replacement buses will be arranged where possible."
An inquiry has been launched by the Transport Accident Investigation Commission, which will take note of multiple elements of the train, railway and crew, the agency said.
Although the investigation was expected to continue after initial on-site analysis, chief investigator of accidents Louise Cook said the process would only impact railway operations for a couple of days.
"“Our investigators would typically spend two to three days on site," she said.
"Their first priority is to gather evidence while it is available. That includes examining and mapping the train and the scene, and speaking with people who witnessed the accident or were involved.”
The return train was scheduled to leave from Arthur's Pass at its usual scheduled time this afternoon.
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