However, when the train driver rounded the corner near Wiri Junction, he spotted the crane over the track and was forced to apply the brakes.
The train stopped 97 metres from the crane.
As a result of the incident, both the train driver and the controller were relieved of their duties while KiwiRail carried out its internal investigation.
According to the TAIC report, the train controller was unable to explain why he changed the freight train's route and his error in failing to block entry to the area of track where the crane was.
It also stated there had been "unauthorised visitors" in the control room with him when he could have been performing a final check of the train control diagram.
In addition to this, the TAIC found instructions given to both the train driver and the controller about the track area undergoing work had been confusing.
Since the incident, KiwiRail has updated its systems so train control diagrams showing where trains need to be re-routed to different tracks due to maintenance work, the report said.
TAIC also noted special bulletins given to relevant train staff outlining track areas under construction needed to be clearer, which KiwiRail advised they had begun to address.
The incident also highlighted problems between staff communication, TAIC said.