An investigation into a near-miss between two passenger trains last year has found concerns about Wellington Railway Station were raised with KiwiRail three years ago.
In November last year, a passenger train to Lower Hutt failed to stop at a red signal and headed towards a train coming from Waikanae.
Both train drivers realised what was happening and stopped the trains 30 metres apart.
Although there was no collision and no one was injured, it caused considerable disruption to services.
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.
"It highlights the difficulties we face in the Wellington Station area. It contains a large number of signals in a constricted space and is also used by all commuter trains operating on the Wellington Rail Network," Moyle said.
"The operation of trains in this area is safe, but we are taking steps to further lower risk.
"The congested nature of the area means there are no easy solutions that could be introduced immediately."
Safety measures in place include a permanent speed restriction of 20km/h around the station, which lowers the chances of a collision if a train was to go through a signal without authorisation.
KiwiRail noted it had also made other improvements in recent years, such as upgrading all signals to high visibility LED units, adding indicator arrows on signals and route indicators, and installing additional train-stops that can activate the brakes on incoming main lines.
The operator said it had been working with the Greater Wellington Regional Council and Transdev Wellington to implement a series of initiatives to improve safety after a TAIC report in 2017 on an earlier incident.
The three are in the process of developing a business case for the resignalling of the entire Wellington Rail Network. KiwiRail said this was at an early stage, but any programme was likely to be costly and lengthy.