KiwiRail has lifted speed restrictions on Wellington's train lines, allowing commuter service timetables to return to normal.
A breakdown of the only machine in the country that can evaluate tracks forced hundreds of trips to be cancelled this week.
KiwiRail said it finished assessing the Kāpiti line on Tuesday night and it would assess the Hutt Valley/Wairarapa Line, the Johnsonville Line and the Melling Line over the next few nights.
In a statement, KiwiRail chief executive Peter Reidy again apologised for the disruption.
"I apologise to the people of the Wellington region again for the disruption over the last three days. We are making changes in KiwiRail to make sure this situation is never repeated."
Earlier in the week, Reidy said a series of failures had led to the disruptions including a mechanical fault with the Track Evaluation Car and scheduling problems.
KiwiRail will be seeking to purchase a new Track Evaluation Car in the next few years which Reidy said would require less maintenance and have less downtime and therefore be more productive.
KiwiRail has ordered a review into the failures which led to the disruptions and the government also announced an urgent review with Transport Minister Michael Wood calling KiwiRail to the Beehive earlier this week to provide an explanation of what happened and the plan to fix it.