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.
KiwiRail/Supplied
A near-collision between two passenger trains at Wellington Station in November 2019 was found to have been caused when a driver was distracted by a radio call, resulting in him running a red light.
Urgent safety improvements are needed at Wellington train station, the Transport Accident Investigation Commission says, after an inexperienced train driver narrowly avoided a collision with an oncoming train last year. The near-miss followed another in 2016, while there had also been 23 incidents of trains failing to stop for a red light when approaching or departing Wellington station in the past decade, the Commission said in a report published on Monday.