There were 315 passengers and three crew on board when the train came off the tracks as it headed into Wellington.
The report said it appeared documentation and bad communication may have resulted in the train being returned to service with the split pins left off.
However, the inquiry is still yet to reach firm conclusions.
Mr Marshall said there were two safety issues identified with Wellington depot.
"First, there were no individual task instructions describing how each safety-critical job was to be done.
"And secondly there was no check sheet associated with each task to record that important steps and checks for the task had been completed.
"Instead, the depot relied on the knowledge of the depot staff to complete each task satisfactorily."
The commission issued Kiwirail with an urgent recommendation to shape up its documentation processes.
KiwiRail chief executive Jim Quinn agreed with the inquiry findings.
"In a safety critical environment like this, such an oversight is of significant concern."
All the recommendations made by the commission have been implemented in the Wellington Depot, he said.
"Heavy component change check sheets have been introduced to take all practicable steps to ensure this kind of incident does not occur again.
"Sign off sheets are required to be completed for each component changed after any of these jobs are finished.
"A post repair inspection process has also been introduced for safety critical items."
Mr Quinn said the depot had an excellent track record.
"Current records show this to be the only [serious] incident in the last 40 years."
Wayne Hastie, the Greater Wellington Regional Council's general manager of public transport, said the additional safety measures were welcome.
"We'll be working closely with them to see how these procedures are going.
"We're all very keen to make sure that incidents like the May 20 derailment don't happen again."
KiwiRail provides urban passenger services in Wellington under contract to the council through their Tranz Metro business.
