The 22-kilometre scheme has been indicatively costed at up to $4 billion.
KiwiRail's bosses have appeared at a select committee to discuss Wellington's rail disruption.
The clean car scheme, $224m in the hole, gets another $100m and focuses on battery electric and plug-in hybrids.
The charges were lodged after complex investigations and come with a fine of up to $1.5 million.
Infrastructure Editor
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articles by Oliver