The Transport Accident Investigation Commission (TAIC) found the driver of the Hutt Valley train was distracted by a radio call and failed to stop.
The commission said it identified safety concerns at the station three years ago and raised these with KiwiRail.
It said KiwiRail should review its arrangements to try to reduce the risk by providing better communication between train drivers.
The commission said if these recommendations were not properly addressed, the risk to the transport system would remain.
In a statement, KiwiRail chief operating officer Todd Moyle said the incident was treated seriously and they accepted it was a significant one, despite no collision or injuries.